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R/SeqFeatR_GUI.R
In SeqFeatR: A Tool to Associate FASTA Sequences and Features
Defines functions
get_label_right
getcsvfile
getFASTAfile
getnexusfile
check_phylo
check_bayes_factor
has_C_allel
check_K
check_offset
check_allels
check_dna
check_ident
generate_example_fasta
generate_example_config
generate_example_config_wo_HLA
save_config
read.config
attach.config
open_tutorial
about
calculate_pos_epi
calculate_pos_epi_further
create_sequence_graphic_G
calculate_co_mut
calculate_co_mut_graphics
calculate_co_mut_graphics_both
calculate_founder
calculate_q_value
shared_mutations
rewrite_shared_mutations
get_freqs
small_manhattan
#R GUI written by Bettina Budeus, rokkaku-fight@gmx.de
#from 2012-07-27 to 2012-?-?
#GUI for scripts to better put data in it
#search for "change" for points where changes are possible
#please check before executing
rm(list = ls())
#libs
require(tcltk)
require(tcltk2)
require(widgetTools)
#----------------------------------------------------------------------------------------------------------------
#loaded objects
calculate_pos_epi_is_running <- FALSE
calculate_pos_epi_further_is_running <- FALSE
calculate_co_mut_is_running <- FALSE
calculate_q_value_is_running <- FALSE
calculate_co_mut_graphics_is_running <- FALSE
calculate_co_mut_graphics_both_is_running <- FALSE
calculate_founder_is_running <- FALSE
create_sequence_graphic_is_running <- FALSE
shared_mutations_is_running <- FALSE
rewrite_shared_mutations_is_running <- FALSE
get_freqs_is_running <- FALSE
small_manhattan_is_running <- FALSE
#----------------------------------------------------------------------------------------------------------------
#Error handling---------------------------------------------------------------------------------------------------
Require <- structure(function(
### checks if a package is available
pkg
### the package to check for
){
if (data.class(result<-try(find.package(pkg),TRUE))=="try-error") {
tkmessageBox(title="An error has occured!",message=paste("Cannot find package\"",pkg,"\". Please install it with install.packages(\"",pkg,"\")",sep=""),icon="error",type="ok")
return (FALSE)
}else{
require(pkg,character.only=TRUE)
return (TRUE)
}
### True if package is there, False if it is not
},ex=function(){
Require(tcltk)
})
#Helper-Functions for the program start---------------------------------------------------------------------------
get_label_right <- function(splitted){
length <- length(splitted[[1]])
if (length>1){
return (paste(splitted[[1]][2], "/../", splitted[[1]][length]))
}
else{
return (splitted[[1]][2])
}
}
getcsvfile <- function(labelT, funct, whichfile) {
loaded_files <- .GlobalEnv[["loaded_files"]]
name <- tclvalue(tkgetOpenFile(filetypes="{{csv Files} {.csv}} {{All files} *}"))
loaded_files[1, whichfile, funct] <- name
splitted <- strsplit(name, "/")
label <- get_label_right(splitted)
tclvalue(labelT) <- label
.GlobalEnv[["loaded_files"]] <- loaded_files
}
getFASTAfile <- function(labelT, funct, whichfile) {
loaded_files <- .GlobalEnv[["loaded_files"]]
name <- tclvalue(tkgetOpenFile(filetypes="{{FASTA Files} {.fasta}} {{All files} *}"))
loaded_files[1, whichfile, funct] <- name
splitted <- strsplit(name, "/")
label <- get_label_right(splitted)
tclvalue(labelT) <- label
.GlobalEnv[["loaded_files"]] <- loaded_files
}
getnexusfile <- function(labelT, funct, whichfile) {
loaded_files <- .GlobalEnv[["loaded_files"]]
name <- tclvalue(tkgetOpenFile(filetypes="{{nexus Files} {.nh}} {{All files} *}"))
loaded_files[1, whichfile, funct] <- name
splitted <- strsplit(name, "/")
label <- get_label_right(splitted)
tclvalue(labelT) <- label
.GlobalEnv[["loaded_files"]] <- loaded_files
}
check_phylo <- function(cbValue, textEntryWidgetKIB){
if (cbValue=="1"){
tkconfigure(textEntryWidgetKIB, state="normal")
}else {
tkconfigure(textEntryWidgetKIB, state="disabled")
}
}
check_bayes_factor <- function(cbValueBayes, cbValueconst, textEntryWidget){
if (cbValueBayes=="1" && cbValueconst=="0"){
tkconfigure(textEntryWidget, state="normal")
}else {
tkconfigure(textEntryWidget, state="disabled")
}
}
has_C_allel <- function(cbValuehasC, textEntryWidgetHCC, textEntryWidgetH1CC, textEntryWidgetH2CC, textEntryWidgetH12CC){
if (cbValuehasC=="1"){
tkconfigure(textEntryWidgetHCC, state="normal")
tkconfigure(textEntryWidgetH1CC, state="normal")
tkconfigure(textEntryWidgetH2CC, state="normal")
tkconfigure(textEntryWidgetH12CC, state="normal")
}else {
tkconfigure(textEntryWidgetHCC, state="disabled")
tkconfigure(textEntryWidgetH1CC, state="disabled")
tkconfigure(textEntryWidgetH2CC, state="disabled")
tkconfigure(textEntryWidgetH12CC, state="disabled")
}
}
check_K <- function(cbValueBayes, cbValueconst, textEntryWidget){
if (cbValueBayes=="1" && cbValueconst=="0"){
tkconfigure(textEntryWidget, state="normal")
}else {
tkconfigure(textEntryWidget, state="disabled")
}
}
check_offset <- function(cbvalues_off, textEntryWidget){
if (cbvalues_off=="1"){
tkconfigure(textEntryWidget, state="normal")
}else {
tkconfigure(textEntryWidget, state="disabled")
}
}
check_allels <- function(cbValue, cMtextEntryWidgetC, button.widget_co2, textEntryWidgetHC, textEntryWidgetH1C, textEntryWidgetH2C, textEntryWidgetH12C, textEntryWidgetHBC, textEntryWidgetH1BC, textEntryWidgetH2BC, textEntryWidgetH12BC) {
if (cbValue=="1"){
tkconfigure(cMtextEntryWidgetC, state="normal")
tkconfigure(button.widget_co2, state="disabled")
tkconfigure(textEntryWidgetHC, state="normal")
tkconfigure(textEntryWidgetH1C, state="normal")
tkconfigure(textEntryWidgetH2C, state="normal")
tkconfigure(textEntryWidgetH12C, state="normal")
tkconfigure(textEntryWidgetHBC, state="normal")
tkconfigure(textEntryWidgetH1BC, state="normal")
tkconfigure(textEntryWidgetH2BC, state="normal")
tkconfigure(textEntryWidgetH12BC, state="normal")
}else {
tkconfigure(cMtextEntryWidgetC, state="disabled")
tkconfigure(button.widget_co2, state="normal")
tkconfigure(textEntryWidgetHC, state="disabled")
tkconfigure(textEntryWidgetH1C, state="disabled")
tkconfigure(textEntryWidgetH2C, state="disabled")
tkconfigure(textEntryWidgetH12C, state="disabled")
tkconfigure(textEntryWidgetHBC, state="disabled")
tkconfigure(textEntryWidgetH1BC, state="disabled")
tkconfigure(textEntryWidgetH2BC, state="disabled")
tkconfigure(textEntryWidgetH12BC, state="disabled")
}
}
check_dna <- function(cbValue) {
if (cbValue=="1"){
}else {
}
}
check_ident <- function(cbValue, textEntryWidgetH, textEntryWidgetH1, textEntryWidgetH12, textEntryWidgetH2, textEntryWidgetHB, textEntryWidgetH1B, textEntryWidgetH12B, textEntryWidgetH2B, textEntryWidgetHC, textEntryWidgetH1C, textEntryWidgetH2C, textEntryWidgetH12C, textEntryWidgetHBC, textEntryWidgetH1BC, textEntryWidgetH2BC, textEntryWidgetH12BC, smtextEntryWidgetX, smtextEntryWidgetH, smtextEntryWidgetH1, smtextEntryWidgetH2, smtextEntryWidgetH12, smtextEntryWidgetHB, smtextEntryWidgetH1B, smtextEntryWidgetH2B, smtextEntryWidgetH12B) {
if (cbValue=="1"){
tkconfigure(textEntryWidgetH, state="disabled")
tkconfigure(textEntryWidgetH1, state="disabled")
tkconfigure(textEntryWidgetH12, state="disabled")
tkconfigure(textEntryWidgetH2, state="disabled")
tkconfigure(textEntryWidgetHB, state="disabled")
tkconfigure(textEntryWidgetH1B, state="disabled")
tkconfigure(textEntryWidgetH12B, state="disabled")
tkconfigure(textEntryWidgetH2B, state="disabled")
tkconfigure(textEntryWidgetHC, state="disabled")
tkconfigure(textEntryWidgetH1C, state="disabled")
tkconfigure(textEntryWidgetH2C, state="disabled")
tkconfigure(textEntryWidgetH12C, state="disabled")
tkconfigure(textEntryWidgetHBC, state="disabled")
tkconfigure(textEntryWidgetH1BC, state="disabled")
tkconfigure(textEntryWidgetH2BC, state="disabled")
tkconfigure(textEntryWidgetH12BC, state="disabled")
tkconfigure(smtextEntryWidgetX, state="normal")
tkconfigure(smtextEntryWidgetH, state="disabled")
tkconfigure(smtextEntryWidgetH1, state="disabled")
tkconfigure(smtextEntryWidgetH2, state="disabled")
tkconfigure(smtextEntryWidgetH12, state="disabled")
tkconfigure(smtextEntryWidgetHB, state="disabled")
tkconfigure(smtextEntryWidgetH1B, state="disabled")
tkconfigure(smtextEntryWidgetH2B, state="disabled")
tkconfigure(smtextEntryWidgetH12B, state="disabled")
}else {
tkconfigure(textEntryWidgetH, state="normal")
tkconfigure(textEntryWidgetH1, state="normal")
tkconfigure(textEntryWidgetH12, state="normal")
tkconfigure(textEntryWidgetH2, state="normal")
tkconfigure(textEntryWidgetHB, state="normal")
tkconfigure(textEntryWidgetH1B, state="normal")
tkconfigure(textEntryWidgetH12B, state="normal")
tkconfigure(textEntryWidgetH2B, state="normal")
tkconfigure(textEntryWidgetHC, state="normal")
tkconfigure(textEntryWidgetH1C, state="normal")
tkconfigure(textEntryWidgetH2C, state="normal")
tkconfigure(textEntryWidgetH12C, state="normal")
tkconfigure(textEntryWidgetHBC, state="normal")
tkconfigure(textEntryWidgetH1BC, state="normal")
tkconfigure(textEntryWidgetH2BC, state="normal")
tkconfigure(textEntryWidgetH12BC, state="normal")
tkconfigure(smtextEntryWidgetX, state="disabled")
tkconfigure(smtextEntryWidgetH, state="normal")
tkconfigure(smtextEntryWidgetH1, state="normal")
tkconfigure(smtextEntryWidgetH2, state="normal")
tkconfigure(smtextEntryWidgetH12, state="normal")
tkconfigure(smtextEntryWidgetHB, state="normal")
tkconfigure(smtextEntryWidgetH1B, state="normal")
tkconfigure(smtextEntryWidgetH2B, state="normal")
tkconfigure(smtextEntryWidgetH12B, state="normal")
}
}
generate_example_fasta <- function(){
sequences <- c("LPDIQGNENMGYQPSWIFCGMETNGSQCLEEMFHCCWINC", "MPDWNQKWGNDHLASINLD-WLKTIQQPGIEKHLRFYENW", "VPDASGKHGIIGMDVTSSMERRHGMVQLPWPAMVWGRPHW", "MPDVRGVGCARRDCLIVHRFCMPFNNQVYCKVWIVYWTYK", "QPDTPKITRKEATAIHKCGIHWQTNCQKLSTVHPFHHQVD", "SWDDFSDFTMVHQWYAQGTLGPYKAMQLKMIFQGVSIMEV", "IPDEPCYCCVKNKILTVEIGVHHAKSQVRRNIDNIRRKTE", "HFST-ICPYIWKMYFTWMGQKLVIQKVNGRTPPHCDECNQ", "SNFT-TTKLRDQHNLYPAGLQEIEHKVDHQILGIYGQIWY", "ETSTALRTQDQTFMLALRANYMVMLKVLDCISVKLFICWR", "DSSTMDAECSTLQRFIWWHAHYAWIRVAKKPYCLDCPYAV", "KKSTLGIARGIQRSHGWYWRQTHCVMVLTPSQHKMGEKSW", "ICSTELCGCLINWPPMQWIVFAHMDDVNDSQTNTCDMRSQ", "GPSTNARTMGGQDCAYMTHTLTKHIWVILAFDPIMIVHKP")
names <- c("P01_HLA_A01_00_B01_02_C22_01", "P02_HLA_A01_00_B01_02_C22_01", "P03_HLA_A01_02_B01_02_C22_01", "P04_HLA_A01_00_B01_02_C22_01", "P05_HLA_A01_00_B01_02_C22_01", "P06_HLA_A01_02_B01_02_C22_01", "P07_HLA_A01_02_B01_02_C22_01", "P08_HLA_A04_03_B04_03_C22_03", "P09_HLA_A04_03_B04_03_C22_01", "P10_HLA_A04_03_B04_03_C22_01", "P11_HLA_A04_03_B04_00_C22_03", "P12_HLA_A04_03_B04_03_C22_01", "P13_HLA_A04_03_B04_00_C22_01", "P14_HLA_A04_03_B04_03_C22_03")
aa_seqs <- AAStringSet(sequences)
names(aa_seqs) <- names
save_file <- tclvalue(tkgetSaveFile(initialfile = "Example_aa.fasta", filetypes = "{{Fasta Files} {.fasta}} {{All files} *}"))
writeXStringSet(aa_seqs, save_file)
}
generate_example_config <- function(){
config <- matrix(c("Number of patients threshold", "Height of horizontal bar", "Height of star level", "HLA-A1", "HLA-A2", "HLA-A3", "HLA-A4", "HLA-B1", "HLA-B2", "HLA-B3", "HLA-B4", "HLA-C1", "HLA-C2", "HLA-C3", "HLA-C4", "C allel", "p-value correction", "Phylogenetic comparison", "offset", "offset_value", "Bayes Factor", "Constant Dirichlet precision parameter", "Dirichlet precision parameter", "One identifier", "window_size", "DNA", "p-value addon", "csv seperator", "number of cases", "position of odds.ratio", "position of p.values", "name for the y-axis label", "frequency", "position of amino acid", "maximum value of y-axis", "intervall of y-axis", "add color information", "bias", "Number of patients threshold_cm", "level for significance", "More than one core", "cmHLA-A1", "cmHLA-A2", "cmHLA-A3", "cmHLA-A4", "cmHLA-B1", "cmHLA-B2", "cmHLA-B3", "cmHLA-B4", "cmp-value correction", "Ratio in subtree", "cMlevel for significance", "space between blocks", "colors of the plot", "name positions", "names", "ticks", "column of first position in first file", "column of second position in first file", "column of values in first file", "column of first position in second file", "column of second position in second file", "column of values in second file", "threshold", "min_number_of_ele_in_tupel", "max_number_of_ele_in_tupel", "column", "column of position", "column of values", "column of aas", "smHLA-A1", "smHLA-A2", "smHLA-A3", "smHLA-A4", "smHLA-B1", "smHLA-B2", "smHLA-B3", "smHLA-B4", "Identifier", "With Allels", "cbWith Allels", "rw column of first position", "rw column of second position", "rw column of values", "rw csv seperator", "rw threshold", "pos_epi_plot", "Epi start", "Epi end", "Epitope Consensus", "gFHLA-A1", "gFHLA-A2", "gFHLA-A3", "gFHLA-A4", "gFHLA-B1", "gFHLA-B2", "gFHLA-B3", "gFHLA-B4", "Feat", "corrected", "axis_break", "1", "0.01", "0.5", "10", "11", "13", "14", "17", "18", "20", "21", "23", "24", "26", "27", "0", "bonferroni", "0", "0", "10", "0", "1", "20", "0", "9", "0", "0.01", ";", "8", "6", "2", "2", "7", "NULL", "4", "0.2", "0", "5","1", "0.01", "0", "10", "11", "13", "14", "17", "18", "20", "21", "bonferroni", "7", "0.01", "5", "wheat, darkblue, black, green", "1,3", "S, F", "1,5", "4", "5", "7", "2", "3", "4", "0.2", "2", "2", "9", "1", "9", "12", "10", "11", "13", "14", "17", "18", "20", "21", "X4", "0", "0", "3", "4", "10", "\\t", "0.1", "TRUE", "1", "8", "LPDIQGNE", "10", "11", "13", "14", "17", "18", "20", "21", "A2", "0", "1,20,40"), ncol=2)
save_file <- tclvalue(tkgetSaveFile(initialfile = "example_config.cfg", filetypes = "{{Config Files} {.cfg}} {{All files} *}"))
write.table(config, save_file, append = FALSE, quote = FALSE, sep = "=", eol = "\n", na = "NA", dec = ".", row.names = FALSE, col.names = FALSE, qmethod = c("escape", "double"), fileEncoding = "")
}
generate_example_config_wo_HLA <- function(){
config <- matrix(c("Number of patients threshold", "Height of horizontal bar", "Height of star level", "p-value correction", "Phylogenetic comparison", "offset", "offset_value", "Bayes Factor", "Constant Dirichlet precision parameter", "Dirichlet precision parameter", "One identifier", "window_size", "DNA", "p-value addon", "csv seperator", "number of cases", "position of odds.ratio", "position of p.values", "name for the y-axis label", "frequency", "position of amino acid", "maximum value of y-axis", "intervall of y-axis", "add color information", "bias", "Number of patients threshold_cm", "level for significance", "More than one core", "cmHLA-A1", "cmHLA-A2", "cmHLA-A3", "cmHLA-A4", "cmHLA-B1", "cmHLA-B2", "cmHLA-B3", "cmHLA-B4", "cmp-value correction", "Ratio in subtree", "cMlevel for significance", "space between blocks", "colors of the plot", "name positions", "names", "ticks", "column of first position in first file", "column of second position in first file", "column of values in first file", "column of first position in second file", "column of second position in second file", "column of values in second file", "threshold", "min_number_of_ele_in_tupel", "max_number_of_ele_in_tupel", "column", "column of position", "column of values", "column of aas", "smHLA-A1", "smHLA-A2", "smHLA-A3", "smHLA-A4", "smHLA-B1", "smHLA-B2", "smHLA-B3", "smHLA-B4", "Identifier", "With Allels", "cbWith Allels", "rw column of first position", "rw column of second position", "rw column of values", "rw csv seperator", "rw threshold", "pos_epi_plot", "Epi start", "Epi end", "Epitope Consensus", "Feat", "corrected", "axis_break", "1", "0.01", "0.5", "bonferroni", "0", "0", "10", "0", "1", "20", "0", "9", "0", "0.01", ";", "8", "6", "2", "2", "7", "NULL", "4", "0.2", "0", "5", "1", "0.01", "0", "10", "11", "13", "14", "17", "18", "20", "21", "bonferroni", "7", "0.01", "5", "wheat, darkblue, black, green", "1,3", "S, F", "1,5", "4", "5", "7", "2", "3", "4", "0.2", "2", "2", "9", "1", "9", "12", "10", "11", "13", "14", "17", "18", "20", "21", "X4", "0", "0", "3", "4", "10", "\\t", "0.1", "TRUE", "1", "8", "LPDIQGNE", "A2", "0", "1,20,40"), ncol=2)
save_file <- tclvalue(tkgetSaveFile(initialfile = "example_config.cfg", filetypes = "{{Config Files} {.cfg}} {{All files} *}"))
write.table(config, save_file, append = FALSE, quote = FALSE, sep = "=", eol = "\n", na = "NA", dec = ".", row.names = FALSE, col.names = FALSE, qmethod = c("escape", "double"), fileEncoding = "")
}
save_config <- function(z){
table <- c()
save_file <- tclvalue(tkgetSaveFile(initialfile = "user_config.cfg", filetypes = "{{Config Files} {.cfg}} {{All files} *}"))
for (i in 1:length(z)){
key <- z[[i]][[2]]
value <- tclvalue(z[[i]][[1]])
table <- rbind(table, c(key, value))
}
write.table(table, save_file, append = FALSE, quote = FALSE, sep = "=", eol = "\n", na = "NA", dec = ".", row.names = FALSE, col.names = FALSE, qmethod = c("escape", "double"), fileEncoding = "")
}
read.config <- function(config){
tryCatch({
key.val <- read.table(config, sep="=", col.names=c("key","value"), as.is=c(1,2))
return (key.val)
}, error = function(err) {tkmessageBox(title="Error",message=paste("No config file loaded. Standard parameters will be used!\n", err),icon="error",type="ok")})
}
attach.config <- function(config){
z <- .GlobalEnv[["z"]]
#print (z)
tryCatch({
con <- read.table(config, sep="=", col.names=c("key","value"), as.is=c(1,2))
#print (con)
for (i in 1:length(z)){
object <- z[[i]][[1]]
object_name <- z[[i]][[2]]
nopt <- con[which(con[,1]==object_name),2]
#print (object)
#print (tclvalue(object))
#print (nopt)
tclvalue(object) <- nopt
}
}, error = function(err) {tkmessageBox(title="Error",message=paste("Error in config file.\n", err),icon="error",type="ok")})
}
open_tutorial <- function(){
epi <- vignette("SeqFeatR")
if (length(epi) > 0){
print (epi)
}
}
about <- function(){
tryCatch({
ReturnVal <- tkmessageBox(title = "About SeqFeatR", message = paste("SeqFeatR Version ", packageVersion("SeqFeatR"), sep=""), icon = "info", type = "ok")
}, error = function(err) {tkmessageBox(title="Error",message=paste("SeqFeatR is not installed"),icon="error",type="ok")})
}
#Functions for the program start-------------------------------------------------------------------------------------------
calculate_pos_epi <- function(tbn, cbValue01, cbValue_0e, textEntryC, textEntryD, textEntryE, textEntryH, textEntryH1, textEntryH2, textEntryH12, textEntryHB, textEntryH1B, textEntryH2B, textEntryH12B, textEntryHCC, textEntryH1CC, textEntryH2CC, textEntryH12CC, cbValue_0eG1C, textEntryIB, txt, icbValue01, textEntryH42B, cbValue_0eG1, cbValue_bayes_factor, cbValue_K, dirichlet_precision_parameter_textEntry){
Require("Biostrings")
Require("plyr")
Require("plotrix")
loaded_files <- .GlobalEnv[["loaded_files"]]
tkconfigure(tbn,cursor="watch")
if (!calculate_pos_epi_is_running){
result <- c()
calculate_pos_epi_is_running <- TRUE
if (data.class(result<-try(find.package("SeqFeatR"),TRUE))=="try-error"){
source("assocpoint.R")
}
tryCatch({ep_wo_set_input_file_known_sequences(loaded_files[1,1,1])}, error = function(err) {tkmessageBox(title="An error has occured!",message="No sequence file",icon="error",type="ok")})
save_name_epi <- tclvalue(tkgetSaveFile(initialfile="epitope_results.pdf",filetypes="{{PDF Files} {.pdf}} {{All files} *}"))
if (!nchar(save_name_epi)){
tkmessageBox(message="No file was selected!")
}
save_name_epi_csv <- tclvalue(tkgetSaveFile(initialfile="epitope_results.csv",filetypes="{{csv Files} {.csv}} {{All files} *}"))
if (!nchar(save_name_epi_csv)){
tkmessageBox(message="No file was selected!")
}
if(as.numeric(tclvalue(textEntryH42B)) <=2){
print ("Beware! Window size smaller than 2! Will be set to 2")
tclvalue(textEntryH42B) <- 2
}
tryCatch({result <- assocpoint(loaded_files[1,1,1], loaded_files[1,2,1], loaded_files[1,3,1], save_name_epi, save_name_epi_csv, as.numeric(tclvalue(cbValue01)), as.numeric(tclvalue(textEntryC)), as.numeric(tclvalue(textEntryD)), as.numeric(tclvalue(textEntryE)), as.numeric(tclvalue(textEntryH)), as.numeric(tclvalue(textEntryH1)), as.numeric(tclvalue(textEntryH2)), as.numeric(tclvalue(textEntryH12)), as.numeric(tclvalue(textEntryHB)), as.numeric(tclvalue(textEntryH1B)), as.numeric(tclvalue(textEntryH2B)), as.numeric(tclvalue(textEntryH12B)), as.numeric(tclvalue(textEntryHCC)), as.numeric(tclvalue(textEntryH1CC)), as.numeric(tclvalue(textEntryH2CC)), as.numeric(tclvalue(textEntryH12CC)), as.logical(as.numeric(cbValue_0eG1C)), tclvalue(textEntryIB), as.logical(as.numeric(cbValue_bayes_factor)), as.logical(as.numeric(cbValue_K)), as.numeric(tclvalue(dirichlet_precision_parameter_textEntry)), as.numeric(tclvalue(cbValue_0e)), loaded_files[1,4,1], as.logical(as.numeric(icbValue01)), as.numeric(tclvalue(textEntryH42B)), as.logical(as.numeric(tclvalue(cbValue_0eG1))) )}, error = function(err) {tkmessageBox(title="An error has occured!",message=paste("No calculation done\n", err),icon="error",type="ok")})
old.option <- (getOption("width", default = NULL))
options(width=2000)
text <- paste(capture.output(print(result)),collapse="\n")
options(width=old.option)
tkconfigure(txt, state="normal")
tryCatch({tkinsert(txt,"end",text)}, error = function(err) {})
tkconfigure(txt, state="disabled")
calculate_pos_epi_is_running <- FALSE
}
tkconfigure(tbn,cursor="arrow")
}
calculate_pos_epi_further <- function(tbn, textEntry_p.value, txt){
Require("Biostrings")
loaded_files <- .GlobalEnv[["loaded_files"]]
tkconfigure(tbn,cursor="watch")
if (!calculate_pos_epi_further_is_running){
result_ef <- c()
calculate_pos_epi_further_is_running <- TRUE
if (data.class(result<-try(find.package("SeqFeatR"),TRUE))=="try-error"){
source("assocpointpair.R")
}
tryCatch({pos_epi_get_input_file_sequences(loaded_files[1,1,4])}, error = function(err) {tkmessageBox(title="An error has occured!",message="No sequence file",icon="error",type="ok")})
tryCatch({pos_epi_get_input_file_pos_epi(loaded_files[1,2,4])}, error = function(err) {tkmessageBox(title="An error has occured!",message="No possible epitope file",icon="error",type="ok")})
tryCatch({pos_epi_get_input_file_mut_core(loaded_files[1,3,4], as.numeric(tclvalue(textEntry_p.value)))}, error = function(err) {tkmessageBox(title="An error has occured!",message="No mutation core file",icon="error",type="ok")})
save_name_ef1 <- tclvalue(tkgetSaveFile(initialfile="co_mut_in_epitopes_result.csv",filetypes="{{csv Files} {.csv}} {{All files} *}"))
if (!nchar(save_name_ef1)){
tkmessageBox(message="No file was selected!")
}
save_name_ef2 <- tclvalue(tkgetSaveFile(initialfile="possible_compensatory_mutation.csv",filetypes="{{csv Files} {.csv}} {{All files} *}"))
if (!nchar(save_name_ef2)){
tkmessageBox(message="No file was selected!")
}
tryCatch({result_ef <- assocpointpair(loaded_files[1,1,4], loaded_files[1,2,4], loaded_files[1,3,4], as.numeric(tclvalue(textEntry_p.value)), save_name_ef1, save_name_ef2)}, error = function(err) {tkmessageBox(title="An error has occured!",message=paste("No calculation done\n", err),icon="error",type="ok")})
old.option <- (getOption("width", default = NULL))
options(width=2000)
text <- paste(capture.output(print (result_ef)),collapse="\n")
options(width=old.option)
tkconfigure(txt, state="normal")
tryCatch({tkinsert(txt,"end",text)}, error = function(err) {})
tkconfigure(txt, state="disabled")
calculate_pos_epi_further_is_running <- FALSE
}
tkconfigure(tbn,cursor="arrow")
}
create_sequence_graphic_G <- function(tbn, BtextEntryA, BtextEntryB, BtextEntryC, BtextEntryD, BtextEntryE, BtextEntryF, BtextEntryG, BtextEntryH, BtextEntryI, txt, BtextEntryJ, BtextEntryK, BtextEntryL){
Require("plotrix")
tkconfigure(tbn,cursor="watch")
loaded_files <- .GlobalEnv[["loaded_files"]]
if (as.character(tclvalue(BtextEntryA)) == "\\t"){
sep <- "\t"
}
else{
sep <- as.character(tclvalue(BtextEntryA))
}
if (!create_sequence_graphic_is_running){
result <- c()
create_sequence_graphic_is_running <- TRUE
if (data.class(result<-try(find.package("SeqFeatR"),TRUE))=="try-error"){
source("orPlot.R")
}
tryCatch({two_wo_set_input_file_known_sequences(loaded_files[1,1,7], sep)}, error = function(err) {tkmessageBox(title="An error has occured!",message="No result input file",icon="error",type="ok")})
save_name_two <- tclvalue(tkgetSaveFile(initialfile="final_graphic",filetypes="{{PDF Files} {.pdf}} {{All files} *}"))
if (!nchar(save_name_two)){
tkmessageBox(message="No file was selected!")
}
tryCatch({result <- orPlot(loaded_files[1,1,7], save_name_two, sep, as.numeric(tclvalue(BtextEntryB)), as.numeric(tclvalue(BtextEntryC)), as.numeric(tclvalue(BtextEntryD)), as.numeric(tclvalue(BtextEntryE)), as.numeric(tclvalue(BtextEntryF)), as.numeric(tclvalue(BtextEntryG)), as.numeric(tclvalue(BtextEntryH)), as.numeric(tclvalue(BtextEntryI)), as.numeric(tclvalue(BtextEntryJ)), as.numeric(tclvalue(BtextEntryK)), tclvalue(BtextEntryL))}, error = function(err) {tkmessageBox(title="An error has occured!",message=paste("No calculation done\n", err),icon="error",type="ok")})
old.option <- (getOption("width", default = NULL))
options(width=2000)
text <- paste(capture.output(print(result)),collapse="\n")
options(width=old.option)
tkconfigure(txt, state="normal")
tryCatch({tkinsert(txt,"end",text)}, error = function(err) {})
tkconfigure(txt, state="disabled")
create_sequence_graphic_is_running <- FALSE
}
tkconfigure(tbn,cursor="arrow")
}
calculate_co_mut <- function(allels, tbn2, txt, cMtextEntryC, cMtextEntryD, cmtextEntryIB, textEntryHC, textEntryH1C, textEntryH2C, textEntryH12C, textEntryHBC, textEntryH1BC, textEntryH2BC, textEntryH12BC, textEntryIB, cbValue01){
Require("Biostrings")
loaded_files <- .GlobalEnv[["loaded_files"]]
tkconfigure(tbn2,cursor="watch")
if (!calculate_co_mut_is_running){
result_co <- c()
calculate_co_mut_is_running <- TRUE
if (allels=="1"){
if (data.class(result<-try(find.package("SeqFeatR"),TRUE))=="try-error"){
source("assocpairfeat.R")
}
tryCatch({cm_get_input_file(loaded_files[1,1,2])}, error = function(err) {tkmessageBox(title="An error has occured!",message="No sequence file",icon="error",type="ok")})
save_name_co_mut <- tclvalue(tkgetSaveFile(initialfile="co_mutation_results.csv",filetypes="{{csv Files} {.csv}} {{All files} *}"))
if (!nchar(save_name_co_mut)){
tkmessageBox(message="No file was selected!")
}
tryCatch({result_co <- assocpairfeat(loaded_files[1,1,2], save_name_co_mut, as.numeric(tclvalue(cbValue01)), as.numeric(tclvalue(cMtextEntryC)), as.numeric(tclvalue(cMtextEntryD)), as.numeric(tclvalue(textEntryHC)), as.numeric(tclvalue(textEntryH1C)), as.numeric(tclvalue(textEntryH2C)), as.numeric(tclvalue(textEntryH12C)), as.numeric(tclvalue(textEntryHBC)), as.numeric(tclvalue(textEntryH1BC)), as.numeric(tclvalue(textEntryH2BC)), as.numeric(tclvalue(textEntryH12BC)), tclvalue(cmtextEntryIB))}, error = function(err) {tkmessageBox(title="An error has occured!",message="No comutation analysis done",icon="error",type="ok")})
}
if (allels=="0"){
if (data.class(result<-try(find.package("SeqFeatR"),TRUE))=="try-error"){
source("assocpair.R")
}
tryCatch({cm_wo_get_input_file_sequences(loaded_files[1,1,2])}, error = function(err) {tkmessageBox(title="An error has occured!",message="No sequence file",icon="error",type="ok")})
tryCatch({cm_wo_get_input_file_consensus(loaded_files[1,2,2])}, error = function(err) {tkmessageBox(title="An error has occured!",message="No consensus file",icon="error",type="ok")})
save_name_co_mut <- tclvalue(tkgetSaveFile(initialfile="co_mutation_results_wo_allels.csv",filetypes="{{csv Files} {.csv}} {{All files} *}"))
if (!nchar(save_name_co_mut)){
tkmessageBox(message="No file was selected!")
}
tryCatch({result_co <- assocpair(loaded_files[1,1,2], loaded_files[1,2,2], save_name_co_mut, as.numeric(tclvalue(cbValue01)), as.numeric(tclvalue(cMtextEntryD)), tclvalue(cmtextEntryIB))}, error = function(err) {tkmessageBox(title="An error has occured!",message=paste("No calculation done\n", err),icon="error",type="ok")})
}
old.option <- (getOption("width", default = NULL))
options(width=2000)
text <- paste(capture.output(print (result_co)),collapse="\n")
options(width=old.option)
tkconfigure(txt, state="normal")
tryCatch({tkinsert(txt,"end",text)}, error = function(err) {})
tkconfigure(txt, state="disabled")
calculate_co_mut_is_running <- FALSE
}
tkconfigure(tbn2,cursor="arrow")
}
calculate_co_mut_graphics <- function(allels, tbn2, cMtextEntryE){
Require("Biostrings")
loaded_files <- .GlobalEnv[["loaded_files"]]
tkconfigure(tbn2,cursor="watch")
if (!calculate_co_mut_graphics_is_running){
calculate_co_mut_graphics_is_running <- TRUE
if (allels=="1"){
if (data.class(result<-try(find.package("SeqFeatR"),TRUE))=="try-error"){
source("visualizepairfeat.R")
}
tryCatch({co_g_get_input_file(loaded_files[1,1,5])}, error = function(err) {tkmessageBox(title="An error has occured!",message="No input file",icon="error",type="ok")})
save_name <- tclvalue(tkgetSaveFile(initialfile="co_mut_g_results.pdf",filetypes="{{PDF Files} {.pdf}} {{All files} *}"))
if (!nchar(save_name)){
tkmessageBox(message="No file was selected!")
}
tryCatch({visualizepairfeat(loaded_files[1,1,5], save_name, as.numeric(tclvalue(cMtextEntryE)))}, error = function(err) {tkmessageBox(title="An error has occured!",message=paste("No calculation done\n", err),icon="error",type="ok")})
}
if (allels=="0"){
if (data.class(result<-try(find.package("SeqFeatR"),TRUE))=="try-error"){
source("visualizepair.R")
}
tryCatch({co_g_get_input_file_wo_allel(loaded_files[1,1,5])}, error = function(err) {tkmessageBox(title="An error has occured!",message="No input file",icon="error",type="ok")})
save_name <- tclvalue(tkgetSaveFile(initialfile="co_mut_g_results_wo_allels.pdf",filetypes="{{PDF Files} {.pdf}} {{All files} *}"))
if (!nchar(save_name)){
tkmessageBox(message="No file was selected!")
}
tryCatch({visualizepair(loaded_files[1,1,5], save_name, as.numeric(tclvalue(cMtextEntryE)))}, error = function(err) {tkmessageBox(title="An error has occured!",message=paste("No calculation done\n", err),icon="error",type="ok")})
}
calculate_co_mut_graphics_is_running <- FALSE
}
tkconfigure(tbn2,cursor="arrow")
}
calculate_co_mut_graphics_both <- function(tbn5, txt, TcMtextEntryE, TcMtextEntryE1, TcMtextEntryE2, TcMtextEntryE3, TcMtextEntryE4, TcMtextEntryE5, TcMtextEntryE6, TcMtextEntryE7, TcMtextEntryE8, TcMtextEntryE9, TcMtextEntryE0){
Require("Biostrings")
loaded_files <- .GlobalEnv[["loaded_files"]]
tkconfigure(tbn5,cursor="watch")
if (!calculate_co_mut_graphics_both_is_running){
calculate_co_mut_graphics_both_is_running <- TRUE
if (data.class(result<-try(find.package("SeqFeatR"),TRUE))=="try-error"){
source("tartan.R")
}
if (loaded_files[1,3,9] == "0"){
with_distance_matrix <- FALSE
} else{
with_distance_matrix <- TRUE
}
tryCatch({co_g_get_input_file_wo_allel(loaded_files[1,1,9])}, error = function(err) {tkmessageBox(title="An error has occured!",message="No input file",icon="error",type="ok")})
tryCatch({co_g_get_input_file2_wo_allel(loaded_files[1,2,9])}, error = function(err) {tkmessageBox(title="An error has occured!",message="No input file",icon="error",type="ok")})
tryCatch({co_g_get_distance_matrix(loaded_files[1,3,9], with_distance_matrix)}, error = function(err) {tkmessageBox(title="An error has occured!",message="No input file",icon="error",type="ok")})
save_name <- tclvalue(tkgetSaveFile(initialfile="co_mut_g_both_results.pdf",filetypes="{{PDF Files} {.pdf}} {{All files} *}"))
if (!nchar(save_name)){
tkmessageBox(message="No file was selected!")
}
list1 <- as.numeric(strsplit(as.character(tclvalue(TcMtextEntryE2)), ",")[[1]])
list2 <- as.numeric(strsplit(as.character(tclvalue(TcMtextEntryE4)), ",")[[1]])
tryCatch({result_tartan <- tartan(loaded_files[1,1,9], loaded_files[1,2,9], save_name, as.numeric(tclvalue(TcMtextEntryE)), strsplit(as.character(tclvalue(TcMtextEntryE1)), ",")[[1]], list1, strsplit(as.character(tclvalue(TcMtextEntryE3)), ",")[[1]], list2, as.numeric(tclvalue(TcMtextEntryE5)), as.numeric(tclvalue(TcMtextEntryE6)), as.numeric(tclvalue(TcMtextEntryE7)), as.numeric(tclvalue(TcMtextEntryE8)), as.numeric(tclvalue(TcMtextEntryE9)), as.numeric(tclvalue(TcMtextEntryE0)), with_distance_matrix, loaded_files[1,3,9] )}, error = function(err) {tkmessageBox(title="An error has occured!",message=paste("No calculation done\n", err),icon="error",type="ok")})
old.option <- (getOption("width", default = NULL))
options(width=2000)
text <- paste(capture.output(print (result_tartan)),collapse="\n")
options(width=old.option)
tkconfigure(txt, state="normal")
tryCatch({tkinsert(txt,"end",text)}, error = function(err) {})
tkconfigure(txt, state="disabled")
calculate_co_mut_graphics_both_is_running <- FALSE
}
tkconfigure(tbn5,cursor="arrow")
}
calculate_founder <- function(tbn2, fetextEntryE, txt){
Require("Biostrings")
Require("phangorn")
loaded_files <- .GlobalEnv[["loaded_files"]]
tkconfigure(tbn2,cursor="watch")
if (!calculate_founder_is_running){
result_fe <- c()
if (data.class(result<-try(find.package("SeqFeatR"),TRUE))=="try-error"){
source("foundereffectfinder.R")
}
calculate_founder_is_running <- TRUE
tryCatch({fe_wo_get_input_file_known_sequences(loaded_files[1,1,6])}, error = function(err) {tkmessageBox(title="An error has occured!",message="No input file",icon="error",type="ok")})
tryCatch({fe_wo_get_input_file_co_mut_results(loaded_files[1,2,6])}, error = function(err) {tkmessageBox(title="An error has occured!",message="No input file",icon="error",type="ok")})
tryCatch({fe_wo_get_input_file_tree(loaded_files[1,3,6])}, error = function(err) {tkmessageBox(title="An error has occured!",message="No input file",icon="error",type="ok")})
save_name_fe <- tclvalue(tkgetSaveFile(initialfile="co_mut_results_from_founder.csv",filetypes="{{csv Files} {.csv}} {{All files} *}"))
if (!nchar(save_name_fe)){
tkmessageBox(message="No file was selected!")
}
tryCatch({result_fe <- foundereffectfinder(loaded_files[1,1,6], loaded_files[1,2,6], loaded_files[1,3,6], save_name_fe, as.numeric(tclvalue(fetextEntryE)))}, error = function(err) {tkmessageBox(title="An error has occured!",message=paste("No calculation done\n", err),icon="error",type="ok")})
old.option <- (getOption("width", default = NULL))
options(width=2000)
text <- paste(capture.output(print (result_fe)),collapse="\n")
options(width=old.option)
tkconfigure(txt, state="normal")
tryCatch({tkinsert(txt,"end",text)}, error = function(err) {})
tkconfigure(txt, state="disabled")
calculate_founder_is_running <- FALSE
}
tkconfigure(tbn2,cursor="arrow")
}
calculate_q_value <- function(tbn3, txt){
Require("Biostrings")
Require("qvalue")
loaded_files <- .GlobalEnv[["loaded_files"]]
tkconfigure(tbn3,cursor="watch")
if (!calculate_q_value_is_running){
result_q <- c()
if (data.class(result<-try(find.package("SeqFeatR"),TRUE))=="try-error"){
source("q-values.R")
}
calculate_q_value_is_running <- TRUE
tryCatch({q_value_set_input_file(loaded_files[1,1,3])}, error = function(err) {tkmessageBox(title="An error has occured!",message="No input file",icon="error",type="ok")})
save_name_q <- tclvalue(tkgetSaveFile(initialfile="csv_with_q_values.csv",filetypes="{{csv Files} {.csv}} {{All files} *}"))
if (!nchar(save_name_q)){
tkmessageBox(message="No file was selected!")
}
tryCatch({result_q <- qvalues(loaded_files[1,1,3], save_name_q)}, error = function(err) {tkmessageBox(title="An error has occured!",message=paste("No calculation done\n", err),icon="error",type="ok")})
old.option <- (getOption("width", default = NULL))
options(width=2000)
text <- paste(capture.output(print (result_q, width="200")),collapse="\n")
options(width=old.option)
tkconfigure(txt, state="normal")
tryCatch({tkinsert(txt,"end",text)}, error = function(err) {})
tkconfigure(txt, state="disabled")
calculate_q_value_is_running <- FALSE
}
tkconfigure(tbn3,cursor="arrow")
}
shared_mutations <- function(tbn5, txt, smtextEntryA, smtextEntryB, smtextEntryC, cbValue_0sM, cbValue_0sM2, smtextEntryE, smtextEntryF, smtextEntryH, smtextEntryH1, smtextEntryH2, smtextEntryH12, smtextEntryHB, smtextEntryH1B, smtextEntryH2B, smtextEntryH12B, icbValue01, smtextEntryidet){
Require("Biostrings")
Require("parallel")
loaded_files <- .GlobalEnv[["loaded_files"]]
tkconfigure(tbn5,cursor="watch")
if (!calculate_q_value_is_running){
result_q <- c()
if (data.class(result<-try(find.package("SeqFeatR"),TRUE))=="try-error"){
source("assoctuple.R")
}
shared_mutations_is_running <- TRUE
tryCatch({sm_wo_set_input_file_ori_sequences(loaded_files[1,1,8])}, error = function(err) {tkmessageBox(title="An error has occured!",message="No input file",icon="error",type="ok")})
tryCatch({sm_wo_set_input_file_epi_results(loaded_files[1,2,8])}, error = function(err) {tkmessageBox(title="An error has occured!",message="No input file",icon="error",type="ok")})
save_name_sm <- tclvalue(tkgetSaveFile(initialfile="shared_mutations.csv",filetypes="{{csv Files} {.csv}} {{All files} *}"))
if (!nchar(save_name_sm)){
tkmessageBox(message="No file was selected!")
}
tryCatch({result_sm <- assoctuple(loaded_files[1,1,8], loaded_files[1,2,8], as.numeric(tclvalue(smtextEntryA)), as.numeric(tclvalue(smtextEntryB)), as.numeric(tclvalue(smtextEntryC)), save_name_sm, as.numeric(tclvalue(cbValue_0sM)), as.numeric(tclvalue(cbValue_0sM2)), as.numeric(tclvalue(smtextEntryE)), as.numeric(tclvalue(smtextEntryF)), as.numeric(tclvalue(smtextEntryH)), as.numeric(tclvalue(smtextEntryH1)), as.numeric(tclvalue(smtextEntryH2)), as.numeric(tclvalue(smtextEntryH12)), as.numeric(tclvalue(smtextEntryHB)), as.numeric(tclvalue(smtextEntryH1B)), as.numeric(tclvalue(smtextEntryH2B)), as.numeric(tclvalue(smtextEntryH12B)), as.logical(as.numeric(icbValue01)), as.character(tclvalue(smtextEntryidet)) )}, error = function(err) {tkmessageBox(title="An error has occured!",message=paste("No calculation done\n", err),icon="error",type="ok")})
old.option <- (getOption("width", default = NULL))
options(width=2000)
text <- paste(capture.output(print (read.csv2(result_sm), width="200")),collapse="\n")
options(width=old.option)
tkconfigure(txt, state="normal")
tryCatch({tkinsert(txt,"end",text)}, error = function(err) {})
tkconfigure(txt, state="disabled")
shared_mutations_is_running <- FALSE
}
tkconfigure(tbn5,cursor="arrow")
}
rewrite_shared_mutations <- function(tbn3, rsmtextEntryE5, rsmtextEntryE6, rsmtextEntryE7, rsmtextEntryA, rsmtextEntryB, txt){
loaded_files <- .GlobalEnv[["loaded_files"]]
tkconfigure(tbn3,cursor="watch")
if (as.character(tclvalue(rsmtextEntryA)) == "\\t"){
sep <- "\t"
}
else{
sep <- as.character(tclvalue(rsmtextEntryA))
}
if (!rewrite_shared_mutations_is_running){
result_q <- c()
if (data.class(result<-try(find.package("SeqFeatR"),TRUE))=="try-error"){
source("rewritetuple.R")
}
rewrite_shared_mutations_is_running <- TRUE
tryCatch({rsm_wo_set_input_file_epi_results(loaded_files[1,1,10], sep)}, error = function(err) {tkmessageBox(title="An error has occured!",message="No input file",icon="error",type="ok")})
save_name_rsm <- tclvalue(tkgetSaveFile(initialfile="rewritten_shared_mutations.csv",filetypes="{{csv Files} {.csv}} {{All files} *}"))
if (!nchar(save_name_rsm)){
tkmessageBox(message="No file was selected!")
}
tryCatch({result_rsm <- rewrite_shared_mutations_result_inner(loaded_files[1,1,10], save_name_rsm, as.numeric(tclvalue(rsmtextEntryE5)), as.numeric(tclvalue(rsmtextEntryE6)), as.numeric(tclvalue(rsmtextEntryE7)), sep, as.numeric(tclvalue(rsmtextEntryB)))}, error = function(err) {tkmessageBox(title="An error has occured!",message=paste("No calculation done\n", err),icon="error",type="ok")})
old.option <- (getOption("width", default = NULL))
options(width=2000)
text <- paste(capture.output(print(result_rsm)),collapse="\n")
options(width=old.option)
tkconfigure(txt, state="normal")
tryCatch({tkinsert(txt,"end",text)}, error = function(err) {})
tkconfigure(txt, state="disabled")
rewrite_shared_mutations_is_running <- FALSE
}
tkconfigure(tbn3,cursor="arrow")
}
get_freqs <- function(tbn3, gFtextEntryC, gFtextEntryD, gFtextEntryF, gFtextEntryH, gFtextEntryH1, gFtextEntryH2, gFtextEntryH12, gFtextEntryHB, gFtextEntryH1B, gFtextEntryH2B, gFtextEntryH12B, txt){
Require("Biostrings")
Require("ggplot2")
loaded_files <- .GlobalEnv[["loaded_files"]]
tkconfigure(tbn3,cursor="watch")
if (!get_freqs_is_running){
result_q <- c()
if (data.class(result<-try(find.package("SeqFeatR"),TRUE))=="try-error"){
source("getfreqs.R")
}
get_freqs_is_running <- TRUE
tryCatch({gF_wo_set_input_file_known_sequences(loaded_files[1,1,11])}, error = function(err) {tkmessageBox(title="An error has occured!",message=geterrmessage(),icon="error",type="ok")})
tryCatch({gF_wo_set_consensus_file_known_sequences(loaded_files[1,2,11])}, error = function(err) {tkmessageBox(title="An error has occured!",message=geterrmessage(),icon="error",type="ok")})
save_name_gF <- tclvalue(tkgetSaveFile(initialfile="Freqs.csv",filetypes="{{csv Files} {.csv}} {{All files} *}"))
if (!nchar(save_name_gF)){
tkmessageBox(message="No file was selected!")
}
save_name_gFp <- tclvalue(tkgetSaveFile(initialfile="Freqs.png",filetypes="{{png Files} {.png}} {{All files} *}"))
if (!nchar(save_name_gFp)){
tkmessageBox(message="No file was selected!")
}
tryCatch({result_gF <- getfreqs(loaded_files[1,1,11], save_name_gF, save_name_gFp, as.numeric(tclvalue(gFtextEntryC)), as.numeric(tclvalue(gFtextEntryD)), loaded_files[1,2,11], as.numeric(tclvalue(gFtextEntryF)), as.numeric(tclvalue(gFtextEntryH)), as.numeric(tclvalue(gFtextEntryH1)), as.numeric(tclvalue(gFtextEntryH2)), as.numeric(tclvalue(gFtextEntryH12)), as.numeric(tclvalue(gFtextEntryHB)), as.numeric(tclvalue(gFtextEntryH1B)), as.numeric(tclvalue(gFtextEntryH2B)), as.numeric(tclvalue(gFtextEntryH12B)) )}, error = function(err) {tkmessageBox(title="An error has occured!",message=paste("No calculation done\n", err),icon="error",type="ok")})
old.option <- (getOption("width", default = NULL))
options(width=2000)
text <- paste(capture.output(print(result_gF)),collapse="\n")
options(width=old.option)
tkconfigure(txt, state="normal")
tryCatch({tkinsert(txt,"end",text)}, error = function(err) {})
tkconfigure(txt, state="disabled")
get_freqs_is_running <- FALSE
}
tkconfigure(tbn3,cursor="arrow")
}
small_manhattan <- function(tbn3, sMtextEntryC, cbValue_0sM, sMtextEntryF, txt){
Require("ggplot2")
Require("scales")
loaded_files <- .GlobalEnv[["loaded_files"]]
tkconfigure(tbn3,cursor="watch")
if (!small_manhattan_is_running){
result_q <- c()
if (data.class(result<-try(find.package("SeqFeatR"),TRUE))=="try-error"){
source("smallmanhattan.R")
}
small_manhattan_is_running <- TRUE
tryCatch({sM_wo_set_input_file_assoc_result(loaded_files[1,1,12])}, error = function(err) {tkmessageBox(title="An error has occured!",message=geterrmessage(),icon="error",type="ok")})
save_name_sM <- tclvalue(tkgetSaveFile(initialfile="smallManhattan.png",filetypes="{{png Files} {.png}} {{All files} *}"))
if (!nchar(save_name_sM)){
tkmessageBox(message="No file was selected!")
}
save_name_sMs <- tclvalue(tkgetSaveFile(initialfile="smallManhattan.svg",filetypes="{{svg Files} {.svg}} {{All files} *}"))
if (!nchar(save_name_sMs)){
tkmessageBox(message="No file was selected!")
}
tryCatch({result_sM <- smallmanhattan(loaded_files[1,1,12], save_name_sM, save_name_sMs, as.character(tclvalue(sMtextEntryC)), as.logical(as.numeric(cbValue_0sM)), as.character(tclvalue(sMtextEntryF)) )}, error = function(err) {tkmessageBox(title="An error has occured!",message=paste("No calculation done\n", err),icon="error",type="ok")})
old.option <- (getOption("width", default = NULL))
options(width=2000)
text <- paste(capture.output(print(result_sM)),collapse="\n")
options(width=old.option)
tkconfigure(txt, state="normal")
tryCatch({tkinsert(txt,"end",text)}, error = function(err) {})
tkconfigure(txt, state="disabled")
small_manhattan_is_running <- FALSE
}
tkconfigure(tbn3,cursor="arrow")
}
#----------------------------------------------------------
SeqFeatR_GUI <- structure(function(
### SeqFeatR GUI to handle the program without command line
){
loaded_files <- array(rep(0, 48), dim=c(1,4,12), dimnames = list("name",c("specific file_1","specific file_2","specific file_3", "specific file_4"),c("pos_epi", "co-mut", "q-value", "pos_e_cal", "graphics_co_mut", "founder_elim", "two_side", "shared_mutations", "co_mut_graphics_both", "rewrite_shared_mutations", "get_freqs", "small_manhattan")))
.GlobalEnv[["loaded_files"]] <- loaded_files
if(length(system.file("extdata", "config.cfg", package="SeqFeatR")) > 1){
con <- read.config(system.file("extdata", "config.cfg", package="SeqFeatR"))
}else {
con <- c()
}
tt <- tktoplevel()
topMenu <- tkmenu(tt) # Create a menu
tkconfigure(tt, menu = topMenu)
fileMenu <- tkmenu(topMenu, tearoff = FALSE)
helpMenu <- tkmenu(topMenu, tearoff = FALSE)
openRecentMenu <- tkmenu(topMenu, tearoff = FALSE)
tkadd(fileMenu, "command", label = "Open config file", command = function() attach.config(tclvalue(tkgetOpenFile(initialfile = "config.cfg", filetypes = "{{Config Files} {.cfg}} {{All files} *}"))))
tkadd(fileMenu, "command", label = "Save config file", command = function() save_config(z))
tkadd(fileMenu, "command", label = "Generate example fasta", command = function() generate_example_fasta())
tkadd(fileMenu, "command", label = "Generate example config", command = function() generate_example_config())
tkadd(fileMenu, "command", label = "Generate example config without HLA", command = function() generate_example_config_wo_HLA())
tkadd(fileMenu, "command", label = "Quit", command = function() tkdestroy(tt))
tkadd(helpMenu, "command", label = "Tutorial", command = function() open_tutorial())
tkadd(helpMenu, "command", label = "About SeqFeatR", command = function() about())
tkadd(topMenu, "cascade", label = "File", menu = fileMenu)
tkadd(topMenu, "cascade", label = "Help", menu = helpMenu)
frameOverall <- tkframe(tt)
frame_progs <- tkframe(frameOverall,relief="groove",borderwidth=2, background="white")
frame_info <- tkframe(frameOverall,relief="groove",borderwidth=2)
frame_bar <- tkframe(frameOverall,relief="sunken",borderwidth=2)
tkpack(frameOverall, fill="both",expand="yes")
tkgrid(frame_progs, sticky="snew")
tkgrid(frame_info)
tkgrid(frame_bar, sticky="snew")
#------------------------------------------------------------------------------------------------------------------------------
#tn <- tkwidget(frame_progs, "ttk::notebook")
#print (.Tcl.args(background="red"))
tcl("ttk::style", "configure", "TNotebook", background="white")
# Make non selected tabs a little darker
tcl("ttk::style", "configure", "TNotebook.Tab", background="lightgrey")
#tcl("ttk::style", "map", "TNotebook.Tab", background=c("active", "skyblue"))
#tcl("ttk::style", "map", "TNotebook.Tab", background=c("active", "red"))
tcl("ttk::style", "map", "TNotebook.Tab", background=c("selected","khaki1"))
tn <- ttknotebook(frame_progs)
#tkwm.resizable(tt, TRUE, TRUE)### FOR WINDOWS COMMENT OUT!!
tkwm.title(tt, "SeqFeatR for the discovery of feature-sequence associations")
tkgrid.columnconfigure(tt,0,weight=1)
tkgrid.rowconfigure(tt,0,weight=1)
tkwm.minsize(tt, "1024", "680")
tkgrid.rowconfigure(frameOverall,1,weight=1, minsize=100)
tkgrid.rowconfigure(frameOverall,0,weight=10, minsize=200)
tkgrid.columnconfigure(frameOverall,0,weight=1, minsize=100)
#tkgrid.configure(frameOverall,sticky='nswe')
tkgrid.rowconfigure(frame_progs,0,weight=1, minsize=20)
tkgrid.rowconfigure(frame_progs,1,weight=100, minsize=100)
tkgrid.columnconfigure(frame_progs,0,weight=1, minsize=10)
tkgrid.configure(frame_progs,sticky='nswe')
tkgrid.rowconfigure(frame_info,1,weight=1, minsize=10)
tkgrid.columnconfigure(frame_info,1,weight=1, minsize=10)
tkgrid.rowconfigure(frame_bar,1,weight=1, minsize=10)
tkgrid.columnconfigure(frame_bar,1,weight=1, minsize=10)
#-----------------------------------------------------------------------------------------------------------------------------
info <- tclVar("*: Please fill in before you hit the corresponding start button. You can generate and load an example configuration under the 'File' menu.")
l <- tklabel(frame_bar, textvariable=info)
tkgrid(l, sticky="snew")
#-----------------------------------------------------------------------------------------------------------------------------
dna <- tkframe(frame_progs)
tkgrid(dna)
tkgrid.rowconfigure(dna,0,weight=0)
tkgrid.columnconfigure(dna,0,weight=0)
cb01 <- tkcheckbutton(dna,command=function()check_dna(cbValu01 <- as.character(tclvalue(cbValue01))), background="#FF6600")
cbValue01 <- tclVar("0")
tkconfigure(cb01,variable=cbValue01)
icb01 <- tkcheckbutton(dna,command=function()check_ident(icbValu01 <- as.character(tclvalue(icbValue01)), textEntryWidgetH, textEntryWidgetH1, textEntryWidgetH12, textEntryWidgetH2, textEntryWidgetHB, textEntryWidgetH1B, textEntryWidgetH12B, textEntryWidgetH2B, textEntryWidgetHC, textEntryWidgetH1C, textEntryWidgetH2C, textEntryWidgetH12C, textEntryWidgetHBC, textEntryWidgetH1BC, textEntryWidgetH2BC, textEntryWidgetH12BC, smtextEntryWidgetX, smtextEntryWidgetH, smtextEntryWidgetH1, smtextEntryWidgetH2, smtextEntryWidgetH12, smtextEntryWidgetHB, smtextEntryWidgetH1B, smtextEntryWidgetH2B, smtextEntryWidgetH12B), background="#FF6600")
icbValue01 <- tclVar("0")
tkconfigure(icb01,variable=icbValue01)
tkgrid(tklabel(dna,text="Fasta files with nucleotides?", background="#FF6600"), cb01, tklabel(dna,text="One feature?", background="#FF6600"), icb01 )
#-----------------------------------------------------------------------------------------------------------------------------
tkgrid.rowconfigure(tn,0,weight=5)
tkgrid.columnconfigure(tn,0,weight=5)
tkgrid.configure(tn,sticky='nswe')
otbn <- ttkframe(tn)
otbn2 <- ttkframe(tn)
otbn3 <- ttkframe(tn)
otbn5 <- ttkframe(tn)
tkadd(tn,otbn,text="Point mutations vs. feature(s)") ### tabid=0
tkadd(tn,otbn2,text="n-Tuple vs. feature(s)") ### tabid=1
tkadd(tn,otbn5,text="Graphics for n-tuple calculations") ### tabid=5
tkadd(tn,otbn3,text="Add-on scripts") ### tabid=3
#------------------------------------------------------------------------------------------------------------------------------
scr <- tkscrollbar(frame_info, repeatinterval=5, command=function(...)tkyview(txt,...))
xscr <- tkscrollbar(frame_info, repeatinterval=5, command=function(...)tkxview(txt,...),orient='horiz')
txt <- tktext(frame_info,bg="white", font="Helvetica", height=15, width=80, wrap="none", yscrollcommand=function(...)tkset(scr,...), xscrollcommand=function(...)tkset(xscr,...))
tkgrid(txt,scr)
tkgrid(xscr)
tkgrid.configure(scr,sticky="ns")
tkgrid.configure(xscr,sticky="ew")
tkconfigure(txt, state="disabled")
tkgrid.rowconfigure(txt,0,weight=1)
tkgrid.columnconfigure(txt,0,weight=1)
tkgrid.configure(txt,sticky='nswe')
#---------------------------------------------------
tkgrid.rowconfigure(otbn,0,weight=1, minsize=100)
tkgrid.columnconfigure(otbn,0,weight=10, minsize=200)
tkgrid.columnconfigure(otbn,1,weight=3, minsize=100)
tbn <- ttkframe(otbn)
helptbn <- ttkframe(otbn)
tkgrid(tbn, helptbn, sticky="snew")
tkgrid.columnconfigure(tbn,0,weight=9)
tkgrid.columnconfigure(helptbn,0,weight=1)
scr1 <- tkscrollbar(tbn, command=function(...)tkyview(txt1,...),bg='white')
txt1 <- tktext(tbn,height=1, width=33, bg='grey')
xscr1 <- tkscrollbar(tbn, command=function(...)tkxview(txt1,...),orient='horiz')
tkconfigure(txt1, yscrollcommand=function(...)tkset(scr1,...), xscrollcommand=function(...)tkset(xscr1,...), state="disabled")
tkpack(scr1,side='right',fill='y')
tkpack(txt1,expand='yes',fill='both')
tkpack(xscr1, side="bottom", fill="x")
sf1 <- tkcanvas(txt1, background="white")
tkwindow.create(txt1, 'end', window=sf1)
epi <- tkframe(sf1,relief="groove",borderwidth=2)
epist <- tkframe(sf1,relief="groove",borderwidth=2)
tkgrid(epi, sticky="e")
tkgrid(epist, sticky="snew")
lb1 <- tklabel(epi, text=paste("Discover associations between point mutations and feature(s)"), background="#FFCC99")
tkgrid (lb1, sticky="snew", columnspan=9)
button.widget_epi1 <- tkbutton(epi,text="Select FASTA file",command=function()getFASTAfile(pElabelText1, 1, 1))
pElabelText <- tclVar("Sequence alignment to analyse *: ")
pElabel1 <- tklabel(epi,text=tclvalue(pElabelText))
tkconfigure(pElabel1,textvariable=pElabelText)
pElabelText1 <- tclVar("")
pElabel2 <- tklabel(epi,text=tclvalue(pElabelText1))
tkconfigure(pElabel2,textvariable=pElabelText1)
tkgrid(pElabel1, pElabel2, button.widget_epi1)
button.widget_epi2 <- tkbutton(epi,text="Select csv file",command=function()getcsvfile(pElabelText1A, 1, 2))
pElabelTextA <- tclVar("Known epitopes: ")
pElabel1A <- tklabel(epi,text=tclvalue(pElabelTextA))
tkconfigure(pElabel1A,textvariable=pElabelTextA)
pElabelText1A <- tclVar("")
pElabel2A <- tklabel(epi,text=tclvalue(pElabelText1A))
tkconfigure(pElabel2A,textvariable=pElabelText1A)
tkgrid(pElabel1A, pElabel2A, button.widget_epi2)
button.widget_epi3 <- tkbutton(epi,text="Select csv file",command=function()getcsvfile(pElabelText1B, 1, 3))
pElabelTextB <- tclVar("Known binding motifs: ")
pElabel1B <- tklabel(epi,text=tclvalue(pElabelTextB))
tkconfigure(pElabel1B,textvariable=pElabelTextB)
button.widget_epi4 <- tkbutton(epi,text="Select FASTA File",command=function()getFASTAfile(pElabelText1D, 1, 4))
pElabelTextD <- tclVar("Reference sequence: ")
pElabel1D <- tklabel(epi,text=tclvalue(pElabelTextD))
tkconfigure(pElabel1D,textvariable=pElabelTextD)
pElabelText1D <- tclVar("")
pElabel2D <- tklabel(epi,text=tclvalue(pElabelText1D))
tkconfigure(pElabel2D,textvariable=pElabelText1D)
tkgrid(pElabel1D, pElabel2D, button.widget_epi4)
pElabelText1B <- tclVar("")
pElabel2B <- tklabel(epi,text=tclvalue(pElabelText1B))
tkconfigure(pElabel2B,textvariable=pElabelText1B)
tkgrid(pElabel1B, pElabel2B, button.widget_epi3)
pElabelTextH <- tclVar("Position of feature A *: ")
pElabel1H <- tklabel(epi,text=tclvalue(pElabelTextH))
if (length(con[which(con[,1]=="HLA-A1"),2]) > 0){
textEntryH <- tclVar(con[which(con[,1]=="HLA-A1"),2])
}else{
textEntryH <- tclVar("")
}
textEntryWidgetH <- tkentry(epi,width=3,textvariable=textEntryH)
pElabelTextH1 <- tclVar("-")
pElabel1H1 <- tklabel(epi,text=tclvalue(pElabelTextH1))
if (length(con[which(con[,1]=="HLA-A2"),2]) > 0){
textEntryH1 <- tclVar(con[which(con[,1]=="HLA-A2"),2])
}else{
textEntryH1 <- tclVar("")
}
textEntryWidgetH1 <- tkentry(epi,width=3,textvariable=textEntryH1)
if (length(con[which(con[,1]=="HLA-A3"),2]) > 0){
textEntryH2 <- tclVar(con[which(con[,1]=="HLA-A3"),2])
}else{
textEntryH2 <- tclVar("")
}
textEntryWidgetH2 <- tkentry(epi,width=3,textvariable=textEntryH2)
pElabelTextH12 <- tclVar("-")
pElabel1H12 <- tklabel(epi,text=tclvalue(pElabelTextH12))
if (length(con[which(con[,1]=="HLA-A4"),2]) > 0){
textEntryH12 <- tclVar(con[which(con[,1]=="HLA-A4"),2])
}else{
textEntryH12 <- tclVar("")
}
textEntryWidgetH12 <- tkentry(epi,width=3,textvariable=textEntryH12)
tkgrid(pElabel1H, textEntryWidgetH, pElabel1H1, textEntryWidgetH1, textEntryWidgetH2, pElabel1H12, textEntryWidgetH12)
pElabelTextHB <- tclVar("Position of feature B *: ")
pElabel1HB <- tklabel(epi,text=tclvalue(pElabelTextHB))
if (length(con[which(con[,1]=="HLA-B1"),2]) > 0){
textEntryHB <- tclVar(con[which(con[,1]=="HLA-B1"),2])
}else{
textEntryHB <- tclVar("")
}
textEntryWidgetHB <- tkentry(epi,width=3,textvariable=textEntryHB)
pElabelTextH1B <- tclVar("-")
pElabel1H1B <- tklabel(epi,text=tclvalue(pElabelTextH1B))
if (length(con[which(con[,1]=="HLA-B2"),2]) > 0){
textEntryH1B <- tclVar(con[which(con[,1]=="HLA-B2"),2])
}else{
textEntryH1B <- tclVar("")
}
textEntryWidgetH1B <- tkentry(epi,width=3,textvariable=textEntryH1B)
if (length(con[which(con[,1]=="HLA-B3"),2]) > 0){
textEntryH2B <- tclVar(con[which(con[,1]=="HLA-B3"),2])
}else{
textEntryH2B <- tclVar("")
}
textEntryWidgetH2B <- tkentry(epi,width=3,textvariable=textEntryH2B)
pElabelTextH12B <- tclVar("-")
pElabel1H12B <- tklabel(epi,text=tclvalue(pElabelTextH12B))
if (length(con[which(con[,1]=="HLA-B4"),2]) > 0){
textEntryH12B <- tclVar(con[which(con[,1]=="HLA-B4"),2])
}else{
textEntryH12B <- tclVar("")
}
textEntryWidgetH12B <- tkentry(epi,width=3,textvariable=textEntryH12B)
tkgrid(pElabel1HB, textEntryWidgetHB, pElabel1H1B, textEntryWidgetH1B, textEntryWidgetH2B, pElabel1H12B, textEntryWidgetH12B)
cb0eG1C <- tkcheckbutton(epi,command=function()has_C_allel(cbValue_0eG1C <- as.character(tclvalue(cbValue_0eG1C)), textEntryWidgetHCC, textEntryWidgetH1CC, textEntryWidgetH2CC, textEntryWidgetH12CC))
if (length(con[which(con[,1]=="C_allel"),2]) > 0){
cbValue_0eG1C <- tclVar(con[which(con[,1]=="has_C"),2])
}else{
cbValue_0eG1C <- tclVar("0")
}
tkconfigure(cb0eG1C,variable=cbValue_0eG1C)
tkgrid(tklabel(epi,text="FASTA header has C allel information?"),cb0eG1C, sticky="snew")
pElabelTextHCC <- tclVar("Position of feature C *: ")
pElabel1HCC <- tklabel(epi,text=tclvalue(pElabelTextHCC))
if (length(con[which(con[,1]=="HLA-C1"),2]) > 0){
textEntryHCC <- tclVar(con[which(con[,1]=="HLA-C1"),2])
}else{
textEntryHCC <- tclVar("")
}
textEntryWidgetHCC <- tkentry(epi,width=3,textvariable=textEntryHCC)
pElabelTextH1CC <- tclVar("-")
pElabel1H1CC <- tklabel(epi,text=tclvalue(pElabelTextH1CC))
if (length(con[which(con[,1]=="HLA-C2"),2]) > 0){
textEntryH1CC <- tclVar(con[which(con[,1]=="HLA-C2"),2])
}else{
textEntryH1CC <- tclVar("")
}
textEntryWidgetH1CC <- tkentry(epi,width=3,textvariable=textEntryH1CC)
if (length(con[which(con[,1]=="HLA-C3"),2]) > 0){
textEntryH2CC <- tclVar(con[which(con[,1]=="HLA-C3"),2])
}else{
textEntryH2CC <- tclVar("")
}
textEntryWidgetH2CC <- tkentry(epi,width=3,textvariable=textEntryH2CC)
pElabelTextH12CC <- tclVar("-")
pElabel1H12CC <- tklabel(epi,text=tclvalue(pElabelTextH12CC))
if (length(con[which(con[,1]=="HLA-C4"),2]) > 0){
textEntryH12CC <- tclVar(con[which(con[,1]=="HLA-C4"),2])
}else{
textEntryH12CC <- tclVar("")
}
textEntryWidgetH12CC <- tkentry(epi,width=3,textvariable=textEntryH12CC)
tkgrid(pElabel1HCC, textEntryWidgetHCC, pElabel1H1CC, textEntryWidgetH1CC, textEntryWidgetH2CC, pElabel1H12CC, textEntryWidgetH12CC)
tkconfigure(textEntryWidgetHCC, state="disabled")
tkconfigure(textEntryWidgetH1CC, state="disabled")
tkconfigure(textEntryWidgetH2CC, state="disabled")
tkconfigure(textEntryWidgetH12CC, state="disabled")
pElabelTextC <- tclVar("Minimal number of members *: ")
pElabel1C <- tklabel(epi,text=tclvalue(pElabelTextC))
if (length(con[which(con[,1]=="Number of patients threshold"),2]) > 0){
textEntryC <- tclVar(con[which(con[,1]=="Number of patients threshold"),2])
}else{
textEntryC <- tclVar("")
}
textEntryWidgetC <- tkentry(epi,textvariable=textEntryC)
tkgrid(pElabel1C, textEntryWidgetC)
pElabelTextD <- tclVar("Height of horizontal line *: ")
pElabel1D2 <- tklabel(epi,text=tclvalue(pElabelTextD))
if (length(con[which(con[,1]=="Height of horizontal bar"),2]) > 0){
textEntryD <- tclVar(con[which(con[,1]=="Height of horizontal bar"),2])
}else{
textEntryD <- tclVar("")
}
textEntryWidgetD <- tkentry(epi,textvariable=textEntryD)
tkgrid(pElabel1D2, textEntryWidgetD)
pElabelTextE <- tclVar("Height of star level *: ")
pElabel1E <- tklabel(epi,text=tclvalue(pElabelTextE))
if (length(con[which(con[,1]=="Height of star level"),2]) > 0){
textEntryE <- tclVar(con[which(con[,1]=="Height of star level"),2])
}else{
textEntryE <- tclVar("")
}
textEntryWidgetE <- tkentry(epi,textvariable=textEntryE)
tkgrid(pElabel1E, textEntryWidgetE)
cb0eG1 <- tkcheckbutton(epi)
if (length(con[which(con[,1]=="pos_epi_plot"),2]) > 0){
cbValue_0eG1 <- tclVar(con[which(con[,1]=="pos_epi_plot"),2])
}else{
cbValue_0eG1 <- tclVar("0")
}
tkconfigure(cb0eG1,variable=cbValue_0eG1)
tkgrid(tklabel(epi,text="Show 'possible epitopes plot' (pdf)?"),cb0eG1, sticky="snew")
pElabelTextH42B <- tclVar("Window size: ")
pElabelH42B <- tklabel(epi,text=tclvalue(pElabelTextH42B))
if (length(con[which(con[,1]=="window_size"),2]) > 0){
textEntryH42B <- tclVar(con[which(con[,1]=="window_size"),2])
}else{
textEntryH42B <- tclVar("")
}
textEntryWidgetH42B <- tkentry(epi,textvariable=textEntryH42B)
tkgrid(pElabelH42B, textEntryWidgetH42B)
pElabelTextIB <- tclVar("P-value correction *: ")
pElabel1IB <- tklabel(epi,text=tclvalue(pElabelTextIB))
ddb <- tkframe(epi)
textEntryIB <- tclVar()
dropdownList(ddb, c("holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none"), textEntryIB, 15, "none")
tkgrid(pElabel1IB, ddb)
cb0e <- tkcheckbutton(epi)#,command=function()check_phylo(cbValu_0e <- as.character(tclvalue(cbValue_0e)), textEntryWidgetKIB))
if (length(con[which(con[,1]=="Phylogenetic comparison"),2]) > 0){
cbValue_0e <- tclVar(con[which(con[,1]=="Phylogenetic comparison"),2])
}else{
cbValue_0e <- tclVar("0")
}
tkconfigure(cb0e,variable=cbValue_0e)
tkgrid(tklabel(epi,text="Check for phylogenetic bias?"),cb0e, sticky="snew")
cbbayes_factor <- tkcheckbutton(epi,command=function()check_bayes_factor(cbValue_bayes_factor <- as.character(tclvalue(cbValue_bayes_factor)), cbValue_K <- as.character(tclvalue(cbValue_K)), textEntryWidgetdirichlet_precision_parameter))
if (length(con[which(con[,1]=="Bayes factor"),2]) > 0){
cbValue_bayes_factor <- tclVar(con[which(con[,1]=="Bayes factor"),2])
}else{
cbValue_bayes_factor <- tclVar("0")
}
tkconfigure(cbbayes_factor,variable=cbValue_bayes_factor)
tkgrid(tklabel(epi,text="Calculation with Bayes Factor?", foreground="goldenrod"),cbbayes_factor, sticky="snew")
cbconK_factor <- tkcheckbutton(epi,command=function()check_K(cbValue_bayes_factor <- as.character(tclvalue(cbValue_bayes_factor)), cbValue_K <- as.character(tclvalue(cbValue_K)), textEntryWidgetdirichlet_precision_parameter))
if (length(con[which(con[,1]=="Bayes factor"),2]) > 0){
cbValue_K <- tclVar(con[which(con[,1]=="constant K"),2])
}else{
cbValue_K <- tclVar("0")
}
tkconfigure(cbconK_factor,variable=cbValue_K)
tkgrid(tklabel(epi,text="Calculation with constant\n Dirichlet precision parameter?", foreground="goldenrod"),cbconK_factor, sticky="snew")
pElabelTextdirichlet_precision_parameter <- tclVar("Dirichlet precision parameter: ")
pElabel1dirichlet_precision_parameter <- tklabel(epi,text=tclvalue(pElabelTextdirichlet_precision_parameter))
if (length(con[which(con[,1]=="Dirichlet precision parameter"),2]) > 0){
dirichlet_precision_parameter_textEntry <- tclVar(con[which(con[,1]=="Dirichlet precision parameter"),2])
}else{
dirichlet_precision_parameter_textEntry <- tclVar("")
}
textEntryWidgetdirichlet_precision_parameter <- tkentry(epi,textvariable=dirichlet_precision_parameter_textEntry)
tkconfigure(textEntryWidgetdirichlet_precision_parameter, state="disabled")
tkgrid(pElabel1dirichlet_precision_parameter, textEntryWidgetdirichlet_precision_parameter)
###set left:
tkgrid.configure(pElabel1,sticky="w")
tkgrid.configure(pElabel1A,sticky="w")
tkgrid.configure(pElabel1B,sticky="w")
tkgrid.configure(pElabel1D,sticky="w")
tkgrid.configure(pElabel1C,sticky="w")
tkgrid.configure(pElabel1D2,sticky="w")
tkgrid.configure(pElabel1E,sticky="w")
tkgrid.configure(pElabel1H,sticky="w")
tkgrid.configure(pElabel1HB,sticky="w")
tkgrid.configure(pElabel1HCC,sticky="w")
tkgrid.configure(pElabel1IB,sticky="w")
tkgrid.configure(pElabelH42B,sticky="w")
tkgrid.configure(pElabel1dirichlet_precision_parameter,sticky="w")
OK.bute1 <- tkbutton(epi,text="Start", foreground = "red",command=function()calculate_pos_epi(tbn, cbValue01, cbValue_0e, textEntryC, textEntryD, textEntryE, textEntryH, textEntryH1, textEntryH2, textEntryH12, textEntryHB, textEntryH1B, textEntryH2B, textEntryH12B, textEntryHCC, textEntryH1CC, textEntryH2CC, textEntryH12CC, as.character(tclvalue(cbValue_0eG1C)), textEntryIB, txt, as.character(tclvalue(icbValue01)), textEntryH42B, cbValue_0eG1, as.character(tclvalue(cbValue_bayes_factor)), as.character(tclvalue(cbValue_K)), dirichlet_precision_parameter_textEntry ))
tkgrid(OK.bute1)
tkgrid.configure(button.widget_epi1, column=8, sticky="e")
tkgrid.configure(button.widget_epi2, column=8, sticky="e")
tkgrid.configure(button.widget_epi3, column=8, sticky="e")
tkgrid.configure(button.widget_epi4, column=8, sticky="e")
tkgrid.configure(OK.bute1, column=8, sticky="e")
tkgrid.configure(pElabel2, column=2, columnspan=6, sticky="w")
tkgrid.configure(pElabel2A, column=2, columnspan=6, sticky="w")
tkgrid.configure(pElabel2B, column=2, columnspan=6, sticky="w")
tkgrid.configure(pElabel2D, column=2, columnspan=6, sticky="w")
tkgrid.configure(textEntryWidgetC, column=2, columnspan=6)
tkgrid.configure(textEntryWidgetD, column=2, columnspan=6)
tkgrid.configure(textEntryWidgetE, column=2, columnspan=6)
tkgrid.configure(ddb, column=2, columnspan=6)
tkgrid.configure(textEntryWidgetH42B, column=2, columnspan=6)
tkgrid.configure(cb0eG1, column=2, columnspan=6)
tkgrid.configure(cb0eG1C, column=2, columnspan=6)
tkgrid.configure(cb0e, column=2, columnspan=6)
tkgrid.configure(cbbayes_factor, column=2, columnspan=6)
tkgrid.configure(cbconK_factor, column=2, columnspan=6)
tkgrid.configure(textEntryWidgetdirichlet_precision_parameter, column=2, columnspan=6)
tkgrid.configure(textEntryWidgetH, column=2)
tkgrid.configure(pElabel1H1, column=3)
tkgrid.configure(textEntryWidgetH1, column=4)
tkgrid.configure(textEntryWidgetH2, column=5)
tkgrid.configure(pElabel1H12, column=6)
tkgrid.configure(textEntryWidgetH12, column=7)
tkgrid.configure(textEntryWidgetHB, column=2)
tkgrid.configure(pElabel1H1B, column=3)
tkgrid.configure(textEntryWidgetH1B, column=4)
tkgrid.configure(textEntryWidgetH2B, column=5)
tkgrid.configure(pElabel1H12B, column=6)
tkgrid.configure(textEntryWidgetH12B, column=7)
tkgrid.configure(textEntryWidgetHCC, column=2)
tkgrid.configure(pElabel1H1CC, column=3)
tkgrid.configure(textEntryWidgetH1CC, column=4)
tkgrid.configure(textEntryWidgetH2CC, column=5)
tkgrid.configure(pElabel1H12CC, column=6)
tkgrid.configure(textEntryWidgetH12CC, column=7)
#-----------------------------------------------------------
lb1 <- tklabel(epist, text=paste("Visualize odds ratios and p-values"), background="#FFCC99")
tkgrid (lb1, sticky="snew", columnspan=8)
Bbutton.widget_epi <- tkbutton(epist,text="Select csv file",command=function()getcsvfile(BpElabelText1, 7, 1))
BpElabelText <- tclVar("Result file from point mutations *: ")
BpElabel1 <- tklabel(epist,text=tclvalue(BpElabelText))
tkconfigure(BpElabel1,textvariable=BpElabelText)
BpElabelText1 <- tclVar("")
BpElabel2 <- tklabel(epist,text=tclvalue(BpElabelText1))
tkconfigure(BpElabel2,textvariable=BpElabelText1)
tkgrid(BpElabel1, BpElabel2, Bbutton.widget_epi)
BpElabelTextA <- tclVar("csv seperator *: ")
BpElabel1A <- tklabel(epist,text=tclvalue(BpElabelTextA))
if (length(con[which(con[,1]=="csv seperator"),2]) > 0){
BtextEntryA <- tclVar(con[which(con[,1]=="csv seperator"),2])
}else{
BtextEntryA <- tclVar("")
}
BtextEntryWidgetA <- tkentry(epist,textvariable=BtextEntryA)
tkgrid(BpElabel1A, BtextEntryWidgetA)
BpElabelTextB <- tclVar("# different features in input file *: ")
BpElabel1B <- tklabel(epist,text=tclvalue(BpElabelTextB))
if (length(con[which(con[,1]=="number of cases"),2]) > 0){
BtextEntryB <- tclVar(con[which(con[,1]=="number of cases"),2])
}else{
BtextEntryB <- tclVar("")
}
BtextEntryWidgetB <- tkentry(epist,textvariable=BtextEntryB)
tkgrid(BpElabel1B, BtextEntryWidgetB)
BpElabelTextC <- tclVar("First column nr. of odds-ratio *: ")
BpElabel1C <- tklabel(epist,text=tclvalue(BpElabelTextC))
if (length(con[which(con[,1]=="position of odds.ratio"),2]) > 0){
BtextEntryC <- tclVar(con[which(con[,1]=="position of odds.ratio"),2])
}else{
BtextEntryC <- tclVar("")
}
BtextEntryWidgetC <- tkentry(epist,textvariable=BtextEntryC)
tkgrid(BpElabel1C, BtextEntryWidgetC)
BpElabelTextD <- tclVar("First column nr. of p-values *: ")
BpElabel1D <- tklabel(epist,text=tclvalue(BpElabelTextD))
if (length(con[which(con[,1]=="position of p.values"),2]) > 0){
BtextEntryD <- tclVar(con[which(con[,1]=="position of p.values"),2])
}else{
BtextEntryD <- tclVar("")
}
BtextEntryWidgetD <- tkentry(epist,textvariable=BtextEntryD)
tkgrid(BpElabel1D, BtextEntryWidgetD)
BpElabelTextE <- tclVar("Column nr. for name (y-axis label) *: ")
BpElabel1E <- tklabel(epist,text=tclvalue(BpElabelTextE))
if (length(con[which(con[,1]=="name for the y-axis label"),2]) > 0){
BtextEntryE <- tclVar(con[which(con[,1]=="name for the y-axis label"),2])
}else{
BtextEntryE <- tclVar("")
}
BtextEntryWidgetE <- tkentry(epist,textvariable=BtextEntryE)
tkgrid(BpElabel1E, BtextEntryWidgetE)
BpElabelTextF <- tclVar("Nr. of columns for one feature *: ")
BpElabel1F <- tklabel(epist,text=tclvalue(BpElabelTextF))
if (length(con[which(con[,1]=="frequency"),2]) > 0){
BtextEntryF <- tclVar(con[which(con[,1]=="frequency"),2])
}else{
BtextEntryF <- tclVar("")
}
BtextEntryWidgetF <- tkentry(epist,textvariable=BtextEntryF)
tkgrid(BpElabel1F, BtextEntryWidgetF)
BpElabelTextG <- tclVar("First column nr. of sequence letter: ")
BpElabel1G <- tklabel(epist,text=tclvalue(BpElabelTextG))
if (length(con[which(con[,1]=="position of amino acid"),2]) > 0){
BtextEntryG <- tclVar(con[which(con[,1]=="position of amino acid"),2])
}else{
BtextEntryG <- tclVar("")
}
BtextEntryWidgetG <- tkentry(epist,textvariable=BtextEntryG)
tkgrid(BpElabel1G, BtextEntryWidgetG)
BpElabelTextH <- tclVar("Maximum value on y-axis *: ")
BpElabel1H <- tklabel(epist,text=tclvalue(BpElabelTextH))
if (length(con[which(con[,1]=="maximum value of y-axis"),2]) > 0){
BtextEntryH <- tclVar(con[which(con[,1]=="maximum value of y-axis"),2])
}else{
BtextEntryH <- tclVar("")
}
BtextEntryWidgetH <- tkentry(epist,textvariable=BtextEntryH)
tkgrid(BpElabel1H, BtextEntryWidgetH)
BpElabelTextI <- tclVar("Ticks on y-axis *: ")
BpElabel1I <- tklabel(epist,text=tclvalue(BpElabelTextI))
if (length(con[which(con[,1]=="intervall of y-axis"),2]) > 0){
BtextEntryI <- tclVar(con[which(con[,1]=="intervall of y-axis"),2])
}else{
BtextEntryI <- tclVar("")
}
BtextEntryWidgetI <- tkentry(epist,textvariable=BtextEntryI)
tkgrid(BpElabel1I, BtextEntryWidgetI)
BpElabelTextJ <- tclVar("First column for add. color information: ")
BpElabel1J <- tklabel(epist,text=tclvalue(BpElabelTextJ))
if (length(con[which(con[,1]=="add color information"),2]) > 0){
BtextEntryJ <- tclVar(con[which(con[,1]=="add color information"),2])
}else{
BtextEntryJ <- tclVar("")
}
BtextEntryWidgetJ <- tkentry(epist,textvariable=BtextEntryJ)
tkgrid(BpElabel1J, BtextEntryWidgetJ)
BpElabelTextK <- tclVar("Bias in color *: ")
BpElabel1K <- tklabel(epist,text=tclvalue(BpElabelTextK))
if (length(con[which(con[,1]=="bias"),2]) > 0){
BtextEntryK <- tclVar(con[which(con[,1]=="bias"),2])
}else{
BtextEntryK <- tclVar("")
}
BtextEntryWidgetK <- tkentry(epist,textvariable=BtextEntryK)
tkgrid(BpElabel1K, BtextEntryWidgetK)
BpElabelTextL <- tclVar("Height equals p-values or odds ratios *: ")
BpElabel1L <- tklabel(epist,text=tclvalue(BpElabelTextL))
ddb2 <- tkframe(epist)
BtextEntryL <- tclVar()
dropdownList(ddb2, c("P", "OR"), BtextEntryL, 15, "P")
tkgrid(BpElabel1L, ddb2)
BOK.bute2 <- tkbutton(epist,text="Start", foreground = "red",command=function()create_sequence_graphic_G(tbn, BtextEntryA, BtextEntryB, BtextEntryC, BtextEntryD, BtextEntryE, BtextEntryF, BtextEntryG, BtextEntryH, BtextEntryI, txt, BtextEntryJ, BtextEntryK, BtextEntryL))
tkgrid(BOK.bute2)
###set left:
tkgrid.configure(BpElabel1, sticky="w")
tkgrid.configure(BpElabel1A, sticky="w")
tkgrid.configure(BpElabel1B, sticky="w")
tkgrid.configure(BpElabel1C, sticky="w")
tkgrid.configure(BpElabel1D, sticky="w")
tkgrid.configure(BpElabel1E, sticky="w")
tkgrid.configure(BpElabel1F, sticky="w")
tkgrid.configure(BpElabel1G, sticky="w")
tkgrid.configure(BpElabel1H, sticky="w")
tkgrid.configure(BpElabel1I, sticky="w")
tkgrid.configure(BpElabel1J, sticky="w")
tkgrid.configure(BpElabel1K, sticky="w")
tkgrid.configure(BpElabel1L, sticky="w")
tkgrid.configure(Bbutton.widget_epi, column=3, sticky="e")
tkgrid.configure(BOK.bute2, column=3, sticky="e")
tkgrid.configure(BpElabel2, column=2)
tkgrid.configure(BtextEntryWidgetA, column=2)
tkgrid.configure(BtextEntryWidgetB, column=2)
tkgrid.configure(BtextEntryWidgetC, column=2)
tkgrid.configure(BtextEntryWidgetD, column=2)
tkgrid.configure(BtextEntryWidgetE, column=2)
tkgrid.configure(BtextEntryWidgetF, column=2)
tkgrid.configure(BtextEntryWidgetG, column=2)
tkgrid.configure(BtextEntryWidgetH, column=2)
tkgrid.configure(BtextEntryWidgetI, column=2)
tkgrid.configure(BtextEntryWidgetJ, column=2)
tkgrid.configure(BtextEntryWidgetK, column=2)
tkgrid.configure(ddb2, column=2)
#--------------------------------------------------------------------------------------------------------------------------------
tkgrid.rowconfigure(otbn2,0,weight=1, minsize=100)
tkgrid.columnconfigure(otbn2,0,weight=10, minsize=200)
tkgrid.columnconfigure(otbn2,1,weight=3, minsize=100)
tbn2 <- ttkframe(otbn2)
helptbn2 <- ttkframe(otbn2)
tkgrid(tbn2, helptbn2, sticky="snew")
tkgrid.columnconfigure(tbn2,0,weight=10)
tkgrid.columnconfigure(helptbn2,0,weight=1)
insidetbn2 <- tkframe(tbn2)
tkpack(insidetbn2,fill='both',expand='yes')
scr2 <- tkscrollbar(insidetbn2, command=function(...)tkyview(txt2,...),bg='white')
txt2 <- tktext(insidetbn2,height=1, width=99,bg='grey')
xscr2 <- tkscrollbar(insidetbn2, command=function(...)tkxview(txt2,...),orient='horiz')
tkconfigure(txt2, yscrollcommand=function(...)tkset(scr2,...), xscrollcommand=function(...)tkset(xscr2,...), state="disabled")
tkpack(scr2,side='right',fill='y')
tkpack(txt2,expand='yes',fill='both')
tkpack(xscr2, side="bottom", fill="x")
sf <- tkcanvas(txt2, background="white")
tkwindow.create(txt2, 'end', window=sf)
cb1 <- tkcheckbutton(sf,command=function()check_allels(cbValu <- as.character(tclvalue(cbValuee)), cMtextEntryWidgetC, button.widget_co2, textEntryWidgetHC, textEntryWidgetH1C, textEntryWidgetH2C, textEntryWidgetH12C, textEntryWidgetHBC, textEntryWidgetH1BC, textEntryWidgetH2BC, textEntryWidgetH12BC), background="#FF6600")
if (length(con[which(con[,1]=="With Allels"),2]) > 0){
cbValuee <- tclVar(con[which(con[,1]=="With Allels"),2])
}else{
cbValuee <- tclVar("0")
}
tkconfigure(cb1,variable=cbValuee)
tkgrid(tklabel(sf,text="Analysis with more than one feature in data (aka HLA allels):", background="#FF6600"),cb1, sticky="snew", columnspan=1)
calc <- tkframe(sf,relief="groove",borderwidth=2)
sm <- tkframe(sf,relief="groove",borderwidth=2)
tkgrid(calc, sticky="snew")
tkgrid(sm, sticky="snew")
heading1 <- tklabel(calc,text="Discovering associations between mutation pairs and features", background="#FFCC99")
tkgrid(heading1, sticky="snew", columnspan=9)
button.widget_co1 <- tkbutton(calc,text="Select FASTA file",command=function()getFASTAfile(cMlabelText1, 2, 1))
cMlabelText <- tclVar("Sequence alignment to analyse *: ")
cMlabel1 <- tklabel(calc,text=tclvalue(cMlabelText))
tkconfigure(cMlabel1,textvariable=cMlabelText)
cMlabelText1 <- tclVar("")
cMlabel2 <- tklabel(calc,text=tclvalue(cMlabelText1))
tkconfigure(cMlabel2,textvariable=cMlabelText1)
tkgrid(cMlabel1, cMlabel2, button.widget_co1)
button.widget_co2 <- tkbutton(calc,text="Select FASTA file",command=function()getFASTAfile(cMlabelText1A, 2, 2))
tkconfigure(button.widget_co2, state="normal")
cMlabelTextA <- tclVar("Sequence consensus *: ")
cMlabel1A <- tklabel(calc,text=tclvalue(cMlabelTextA))
tkconfigure(cMlabel1A,textvariable=cMlabelTextA)
cMlabelText1A <- tclVar("")
cMlabel2A <- tklabel(calc,text=tclvalue(cMlabelText1A))
tkconfigure(cMlabel2A,textvariable=cMlabelText1A)
tkgrid(cMlabel1A, cMlabel2A, button.widget_co2)
cMlabelTextC <- tclVar("Minimal number of members *: ")
cMlabel1C <- tklabel(calc,text=tclvalue(cMlabelTextC))
if (length(con[which(con[,1]=="Number of patients threshold_cm"),2]) > 0){
cMtextEntryC <- tclVar(con[which(con[,1]=="Number of patients threshold_cm"),2])
}else{
cMtextEntryC <- tclVar("")
}
cMtextEntryWidgetC <- tkentry(calc,textvariable=cMtextEntryC)
tkconfigure(cMtextEntryWidgetC, state="disabled")
tkgrid(cMlabel1C, cMtextEntryWidgetC)
cMlabelTextD <- tclVar("Significance level *: ")
cMlabel1D <- tklabel(calc,text=tclvalue(cMlabelTextD))
if (length(con[which(con[,1]=="level for significance"),2]) > 0){
cMtextEntryD <- tclVar(con[which(con[,1]=="level for significance"),2])
}else{
cMtextEntryD <- tclVar("")
}
cMtextEntryWidgetD <- tkentry(calc,textvariable=cMtextEntryD)
tkgrid(cMlabel1D, cMtextEntryWidgetD)
cbm <- tkcheckbutton(calc)
if (length(con[which(con[,1]=="More than one core"),2]) > 0){
cbValuem <- tclVar(con[which(con[,1]=="More than one core"),2])
}else{
cbValuem <- tclVar("0")
}
tkconfigure(cbm,variable=cbValuem)
tkgrid(tklabel(calc,text="Use more than one core?"),cbm)
cMlabelTextHC <- tclVar("Position of feature A *: ")
cMlabel1HC <- tklabel(calc,text=tclvalue(cMlabelTextHC))
if (length(con[which(con[,1]=="cmHLA-A1"),2]) > 0){
textEntryHC <- tclVar(con[which(con[,1]=="cmHLA-A1"),2])
}else{
textEntryHC <- tclVar("")
}
textEntryWidgetHC <- tkentry(calc,width=3,textvariable=textEntryHC)
cMlabelTextH1C <- tclVar("-")
cMlabel1H1C <- tklabel(calc,text=tclvalue(cMlabelTextH1C))
if (length(con[which(con[,1]=="cmHLA-A2"),2]) > 0){
textEntryH1C <- tclVar(con[which(con[,1]=="cmHLA-A2"),2])
}else{
textEntryH1C <- tclVar("")
}
textEntryWidgetH1C <- tkentry(calc,width=3,textvariable=textEntryH1C)
if (length(con[which(con[,1]=="cmHLA-A3"),2]) > 0){
textEntryH2C <- tclVar(con[which(con[,1]=="cmHLA-A3"),2])
}else{
textEntryH2C <- tclVar("")
}
textEntryWidgetH2C <- tkentry(calc,width=3,textvariable=textEntryH2C)
cMlabelTextH12C <- tclVar("-")
cMlabel1H12C <- tklabel(calc,text=tclvalue(cMlabelTextH12C))
if (length(con[which(con[,1]=="cmHLA-A4"),2]) > 0){
textEntryH12C <- tclVar(con[which(con[,1]=="cmHLA-A4"),2])
}else{
textEntryH12C <- tclVar("")
}
textEntryWidgetH12C <- tkentry(calc,width=3,textvariable=textEntryH12C)
tkgrid(cMlabel1HC, textEntryWidgetHC, cMlabel1H1C, textEntryWidgetH1C, textEntryWidgetH2C, cMlabel1H12C, textEntryWidgetH12C)
tkconfigure(textEntryWidgetHC, state="disabled")
tkconfigure(textEntryWidgetH1C, state="disabled")
tkconfigure(textEntryWidgetH2C, state="disabled")
tkconfigure(textEntryWidgetH12C, state="disabled")
cMlabelTextHBC <- tclVar("Position of feature B *: ")
cMlabel1HBC <- tklabel(calc,text=tclvalue(cMlabelTextHBC))
if (length(con[which(con[,1]=="cmHLA-B1"),2]) > 0){
textEntryHBC <- tclVar(con[which(con[,1]=="cmHLA-B1"),2])
}else{
textEntryHBC <- tclVar("")
}
textEntryWidgetHBC <- tkentry(calc,width=3,textvariable=textEntryHBC)
cMlabelTextH1BC <- tclVar("-")
cMlabel1H1BC <- tklabel(calc,text=tclvalue(cMlabelTextH1BC))
if (length(con[which(con[,1]=="cmHLA-B2"),2]) > 0){
textEntryH1BC <- tclVar(con[which(con[,1]=="cmHLA-B2"),2])
}else{
textEntryH1BC <- tclVar("")
}
textEntryWidgetH1BC <- tkentry(calc,width=3,textvariable=textEntryH1BC)
if (length(con[which(con[,1]=="cmHLA-B3"),2]) > 0){
textEntryH2BC <- tclVar(con[which(con[,1]=="cmHLA-B3"),2])
}else{
textEntryH2BC <- tclVar("")
}
textEntryWidgetH2BC <- tkentry(calc,width=3,textvariable=textEntryH2BC)
cMlabelTextH12BC <- tclVar("-")
cMlabel1H12BC <- tklabel(calc,text=tclvalue(cMlabelTextH12BC))
if (length(con[which(con[,1]=="cmHLA-B4"),2]) > 0){
textEntryH12BC <- tclVar(con[which(con[,1]=="cmHLA-B4"),2])
}else{
textEntryH12BC <- tclVar("")
}
textEntryWidgetH12BC <- tkentry(calc,width=3,textvariable=textEntryH12BC)
tkgrid(cMlabel1HBC, textEntryWidgetHBC, cMlabel1H1BC, textEntryWidgetH1BC, textEntryWidgetH2BC, cMlabel1H12BC, textEntryWidgetH12BC)
tkconfigure(textEntryWidgetHBC, state="disabled")
tkconfigure(textEntryWidgetH1BC, state="disabled")
tkconfigure(textEntryWidgetH2BC, state="disabled")
tkconfigure(textEntryWidgetH12BC, state="disabled")
cmlabelTextIB <- tclVar("P-value correction *: ")
cmlabel1IB <- tklabel(calc,text=tclvalue(cmlabelTextIB))
ddbc <- tkframe(calc)
cmtextEntryIB <- tclVar()
dropdownList(ddbc, c("holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none"), cmtextEntryIB, 15, "none")
tkgrid(cmlabel1IB, ddbc)
OK.but21 <- tkbutton(calc,text="Start", foreground = "red",command=function()calculate_co_mut(cbVal <- as.character(tclvalue(cbValuee)), tbn2, txt, cMtextEntryC, cMtextEntryD, cmtextEntryIB, textEntryHC, textEntryH1C, textEntryH2C, textEntryH12C, textEntryHBC, textEntryH1BC, textEntryH2BC, textEntryH12BC, cmtextEntryIB, cbValue01))
tkgrid(OK.but21)
###set left:
tkgrid.configure(cMlabel1, sticky="w")
tkgrid.configure(cMlabel1A, sticky="w")
tkgrid.configure(cMlabel1C, sticky="w")
tkgrid.configure(cMlabel1D, sticky="w")
tkgrid.configure(cMlabel1HC, sticky="w")
tkgrid.configure(cMlabel1HBC, sticky="w")
tkgrid.configure(cmlabel1IB, sticky="w")
tkgrid.configure(button.widget_co1, column=8, sticky="e")
tkgrid.configure(button.widget_co2, column=8, sticky="e")
tkgrid.configure(OK.but21, column=8, sticky="e")
tkgrid.configure(cMlabel2, column=2, columnspan=6, sticky="w")
tkgrid.configure(cMlabel2A, column=2, columnspan=6, sticky="w")
tkgrid.configure(cMtextEntryWidgetC, column=2, columnspan=6)
tkgrid.configure(cMtextEntryWidgetD, column=2, columnspan=6)
tkgrid.configure(cbm, column=2, columnspan=6)
tkgrid.configure(ddbc, column=2, columnspan=6)
tkgrid.configure(textEntryWidgetHC, column=2)
tkgrid.configure(cMlabel1H1C, column=3)
tkgrid.configure(textEntryWidgetH1C, column=4)
tkgrid.configure(textEntryWidgetH2C, column=5)
tkgrid.configure(cMlabel1H12C, column=6)
tkgrid.configure(textEntryWidgetH12C, column=7)
tkgrid.configure(textEntryWidgetHBC, column=2)
tkgrid.configure(cMlabel1H1BC, column=3)
tkgrid.configure(textEntryWidgetH1BC, column=4)
tkgrid.configure(textEntryWidgetH2BC, column=5)
tkgrid.configure(cMlabel1H12BC, column=6)
tkgrid.configure(textEntryWidgetH12BC, column=7)
#-------------------------------
heading4 <- tklabel(sm,text="Discovering associations between n-tuple of mutations and features", background="#FFCC99")
tkgrid(heading4, sticky="snew", columnspan=9)
button.widget_sm1 <- tkbutton(sm,text="Select FASTA file",command=function()getFASTAfile(smlabelText1, 8, 1))
smlabelText <- tclVar("Sequence alignment to analyse: ")
smlabel1 <- tklabel(sm,text=tclvalue(smlabelText))
tkconfigure(smlabel1,textvariable=smlabelText)
smlabelText1 <- tclVar("")
smlabel12 <- tklabel(sm,text=tclvalue(smlabelText1))
tkconfigure(smlabel12,textvariable=smlabelText1)
tkgrid(smlabel1, smlabel12, button.widget_sm1)
button.widget_sm2 <- tkbutton(sm,text="Select csv file",command=function()getcsvfile(smlabelText3, 8, 2))
smlabelText2 <- tclVar("Results from \"point mutations\" *:")
smlabel2 <- tklabel(sm,text=tclvalue(smlabelText2))
tkconfigure(smlabel2,textvariable=smlabelText2)
smlabelText3 <- tclVar("")
smlabel3 <- tklabel(sm,text=tclvalue(smlabelText3))
tkconfigure(smlabel3,textvariable=smlabelText3)
tkgrid(smlabel2, smlabel3, button.widget_sm2)
smlabelTextA <- tclVar("Significance value *:")
smlabel1A <- tklabel(sm,text=tclvalue(smlabelTextA))
if (length(con[which(con[,1]=="threshold"),2]) > 0){
smtextEntryA <- tclVar(con[which(con[,1]=="threshold"),2])
}else{
smtextEntryA <- tclVar("")
}
smtextEntryWidgetA <- tkentry(sm,textvariable=smtextEntryA)
tkgrid(smlabel1A, smtextEntryWidgetA)
smlabelTextB <- tclVar("Min. nr. of elements in tuple *:")
smlabel1B <- tklabel(sm,text=tclvalue(smlabelTextB))
if (length(con[which(con[,1]=="min_number_of_ele_in_tupel"),2]) > 0){
smtextEntryB <- tclVar(con[which(con[,1]=="min_number_of_ele_in_tupel"),2])
}else{
smtextEntryB <- tclVar("")
}
smtextEntryWidgetB <- tkentry(sm,textvariable=smtextEntryB)
tkgrid(smlabel1B, smtextEntryWidgetB)
smlabelTextC <- tclVar("Max. nr. of elements in tuple *:")
smlabel1C <- tklabel(sm,text=tclvalue(smlabelTextC))
if (length(con[which(con[,1]=="max_number_of_ele_in_tuple"),2]) > 0){
smtextEntryC <- tclVar(con[which(con[,1]=="max_number_of_ele_in_tuple"),2])
}else{
smtextEntryC <- tclVar("")
}
smtextEntryWidgetC <- tkentry(sm,textvariable=smtextEntryC)
tkgrid(smlabel1C, smtextEntryWidgetC)
smlabelTextD <- tclVar("Column nr. of identifier *:")
smlabel1D <- tklabel(sm,text=tclvalue(smlabelTextD))
if (length(con[which(con[,1]=="column"),2]) > 0){
cbValue_0sM <- tclVar(con[which(con[,1]=="column"),2])
}else{
cbValue_0sM <- tclVar("")
}
smtextEntryWidgetD <- tkentry(sm,textvariable=cbValue_0sM)
tkgrid(smlabel1D, smtextEntryWidgetD)
smlabelTextD2 <- tclVar("Column nr. of alignment pos *:")
smlabel1D2 <- tklabel(sm,text=tclvalue(smlabelTextD2))
if (length(con[which(con[,1]=="column of position"),2]) > 0){
cbValue_0sM2 <- tclVar(con[which(con[,1]=="column of position"),2])
}else{
cbValue_0sM2 <- tclVar("")
}
smtextEntryWidgetD2 <- tkentry(sm,textvariable=cbValue_0sM2)
tkgrid(smlabel1D2, smtextEntryWidgetD2)
smlabelTextE <- tclVar("Column nr. of p-values *:")
smlabel1E <- tklabel(sm,text=tclvalue(smlabelTextE))
if (length(con[which(con[,1]=="column of values"),2]) > 0){
smtextEntryE <- tclVar(con[which(con[,1]=="column of values"),2])
}else{
smtextEntryE <- tclVar("")
}
smtextEntryWidgetE <- tkentry(sm,textvariable=smtextEntryE)
tkgrid(smlabel1E, smtextEntryWidgetE)
smlabelTextF <- tclVar("Column nr. of aa/nt *:")
smlabel1F <- tklabel(sm,text=tclvalue(smlabelTextF))
if (length(con[which(con[,1]=="column of aas"),2]) > 0){
smtextEntryF <- tclVar(con[which(con[,1]=="column of aas"),2])
}else{
smtextEntryF <- tclVar("")
}
smtextEntryWidgetF <- tkentry(sm,textvariable=smtextEntryF)
tkgrid(smlabel1F, smtextEntryWidgetF)
smlabelTextH <- tclVar("Position of feature A *:")
smlabel1H <- tklabel(sm,text=tclvalue(smlabelTextH))
if (length(con[which(con[,1]=="smHLA-A1"),2]) > 0){
smtextEntryH <- tclVar(con[which(con[,1]=="smHLA-A1"),2])
}else{
smtextEntryH <- tclVar("")
}
smtextEntryWidgetH <- tkentry(sm,width=3,textvariable=smtextEntryH)
smlabelTextH1 <- tclVar("-")
smlabel1H1 <- tklabel(sm,text=tclvalue(smlabelTextH1))
if (length(con[which(con[,1]=="smHLA-A2"),2]) > 0){
smtextEntryH1 <- tclVar(con[which(con[,1]=="smHLA-A2"),2])
}else{
smtextEntryH1 <- tclVar("")
}
smtextEntryWidgetH1 <- tkentry(sm,width=3,textvariable=smtextEntryH1)
if (length(con[which(con[,1]=="smHLA-A3"),2]) > 0){
smtextEntryH2 <- tclVar(con[which(con[,1]=="smHLA-A3"),2])
}else{
smtextEntryH2 <- tclVar("")
}
smtextEntryWidgetH2 <- tkentry(sm,width=3,textvariable=smtextEntryH2)
smlabelTextH12 <- tclVar("-")
smlabel1H12 <- tklabel(sm,text=tclvalue(smlabelTextH12))
if (length(con[which(con[,1]=="smHLA-A4"),2]) > 0){
smtextEntryH12 <- tclVar(con[which(con[,1]=="smHLA-A4"),2])
}else{
smtextEntryH12 <- tclVar("")
}
smtextEntryWidgetH12 <- tkentry(sm,width=3,textvariable=textEntryH12)
tkgrid(smlabel1H, smtextEntryWidgetH, smlabel1H1, smtextEntryWidgetH1, smtextEntryWidgetH2, smlabel1H12, smtextEntryWidgetH12)
smlabelTextHB <- tclVar("Position of feature B *:")
smlabel1HB <- tklabel(sm,text=tclvalue(smlabelTextHB))
if (length(con[which(con[,1]=="smHLA-B1"),2]) > 0){
smtextEntryHB <- tclVar(con[which(con[,1]=="smHLA-B1"),2])
}else{
smtextEntryHB <- tclVar("")
}
smtextEntryWidgetHB <- tkentry(sm,width=3,textvariable=smtextEntryHB)
smlabelTextH1B <- tclVar("-")
smlabel1H1B <- tklabel(sm,text=tclvalue(smlabelTextH1B))
if (length(con[which(con[,1]=="smHLA-B2"),2]) > 0){
smtextEntryH1B <- tclVar(con[which(con[,1]=="smHLA-B2"),2])
}else{
smtextEntryH1B <- tclVar("")
}
smtextEntryWidgetH1B <- tkentry(sm,width=3,textvariable=smtextEntryH1B)
if (length(con[which(con[,1]=="smHLA-B3"),2]) > 0){
smtextEntryH2B <- tclVar(con[which(con[,1]=="smHLA-B3"),2])
}else{
smtextEntryH2B <- tclVar("")
}
smtextEntryWidgetH2B <- tkentry(sm,width=3,textvariable=smtextEntryH2B)
smlabelTextH12B <- tclVar("-")
smlabel1H12B <- tklabel(sm,text=tclvalue(smlabelTextH12B))
if (length(con[which(con[,1]=="smHLA-B4"),2]) > 0){
smtextEntryH12B <- tclVar(con[which(con[,1]=="smHLA-B4"),2])
}else{
smtextEntryH12B <- tclVar("")
}
smtextEntryWidgetH12B <- tkentry(sm,width=3,textvariable=smtextEntryH12B)
tkgrid(smlabel1HB, smtextEntryWidgetHB, smlabel1H1B, smtextEntryWidgetH1B, smtextEntryWidgetH2B, smlabel1H12B, smtextEntryWidgetH12B)
smlabelTextX <- tclVar("Identifier (if only one feature): ")
smlabelX <- tklabel(sm,text=tclvalue(smlabelTextX))
if (length(con[which(con[,1]=="Identifier"),2]) > 0){
smtextEntryidet <- tclVar(con[which(con[,1]=="Identifier"),2])
}else{
smtextEntryidet <- tclVar("")
}
smtextEntryWidgetX <- tkentry(sm,textvariable=smtextEntryidet)
tkgrid(smlabelX, smtextEntryWidgetX)
tkconfigure(smtextEntryWidgetX, state="disabled")
OK.but4 <- tkbutton(sm,text="Start", foreground = "red",command=function()shared_mutations(tbn2, txt, smtextEntryA, smtextEntryB, smtextEntryC, cbValue_0sM, cbValue_0sM2, smtextEntryE, smtextEntryF, smtextEntryH, smtextEntryH1, smtextEntryH2, smtextEntryH12, smtextEntryHB, smtextEntryH1B, smtextEntryH2B, smtextEntryH12B, as.character(tclvalue(icbValue01)), smtextEntryidet ))
tkgrid(OK.but4)
###set left:
tkgrid.configure(smlabel1, sticky="w")
tkgrid.configure(smlabel2, sticky="w")
tkgrid.configure(smlabel1A, sticky="w")
tkgrid.configure(smlabel1B, sticky="w")
tkgrid.configure(smlabel1C, sticky="w")
tkgrid.configure(smlabel1D, sticky="w")
tkgrid.configure(smlabel1D2, sticky="w")
tkgrid.configure(smlabel1E, sticky="w")
tkgrid.configure(smlabel1F, sticky="w")
tkgrid.configure(smlabel1H, sticky="w")
tkgrid.configure(smlabel1HB, sticky="w")
tkgrid.configure(smlabelX, sticky="w")
tkgrid.configure(button.widget_sm1, column=8, sticky="e")
tkgrid.configure(button.widget_sm2, column=8, sticky="e")
tkgrid.configure(OK.but4, column=8, sticky="e")
tkgrid.configure(smlabel12, column=2, columnspan=6)
tkgrid.configure(smlabel3, column=2, columnspan=6)
tkgrid.configure(smtextEntryWidgetA, column=2, columnspan=6)
tkgrid.configure(smtextEntryWidgetB, column=2, columnspan=6)
tkgrid.configure(smtextEntryWidgetC, column=2, columnspan=6)
tkgrid.configure(smtextEntryWidgetD, column=2, columnspan=6)
tkgrid.configure(smtextEntryWidgetD2, column=2, columnspan=6)
tkgrid.configure(smtextEntryWidgetE, column=2, columnspan=6)
tkgrid.configure(smtextEntryWidgetF, column=2, columnspan=6)
tkgrid.configure(smtextEntryWidgetX, column=2, columnspan=6)
tkgrid.configure(smtextEntryWidgetH, column=2)
tkgrid.configure(smlabel1H1, column=3)
tkgrid.configure(smtextEntryWidgetH1, column=4)
tkgrid.configure(smtextEntryWidgetH2, column=5)
tkgrid.configure(smlabel1H12, column=6)
tkgrid.configure(smtextEntryWidgetH12, column=7)
tkgrid.configure(smtextEntryWidgetHB, column=2)
tkgrid.configure(smlabel1H1B, column=3)
tkgrid.configure(smtextEntryWidgetH1B, column=4)
tkgrid.configure(smtextEntryWidgetH2B, column=5)
tkgrid.configure(smlabel1H12B, column=6)
tkgrid.configure(smtextEntryWidgetH12B, column=7)
#--------------------------------------------------------------------------------------------------------------------------------
tkgrid.rowconfigure(otbn5,0,weight=1, minsize=100)
tkgrid.columnconfigure(otbn5,0,weight=10, minsize=200)
tkgrid.columnconfigure(otbn5,1,weight=3, minsize=100)
tbn5 <- ttkframe(otbn5)
helptbn5 <- ttkframe(otbn5)
tkgrid(tbn5, helptbn5, sticky="snew")
tkgrid.columnconfigure(tbn5,0,weight=10)
tkgrid.columnconfigure(helptbn5,0,weight=1)
scr3 <- tkscrollbar(tbn5, command=function(...)tkyview(txt3,...),bg='white')
txt3 <- tktext(tbn5,height=1,width=55,bg='grey')
xscr3 <- tkscrollbar(tbn5, command=function(...)tkxview(txt3,...),orient='horiz')
tkconfigure(txt3, yscrollcommand=function(...)tkset(scr3,...), xscrollcommand=function(...)tkset(xscr3,...), state="disabled")
tkpack(scr3,side='right',fill='y')
tkpack(txt3,expand='yes',fill='both')
tkpack(xscr3, side="bottom", fill="x")
sf3 <- tkcanvas(txt3, background="white")
tkwindow.create(txt3, 'end', window=sf3)
cb <- tkcheckbutton(sf3,command=function()check_allels(cbValu <- as.character(tclvalue(cbValue)), cMtextEntryWidgetC, button.widget_co2, textEntryWidgetHC, textEntryWidgetH1C, textEntryWidgetH2C, textEntryWidgetH12C, textEntryWidgetHBC, textEntryWidgetH1BC, textEntryWidgetH2BC, textEntryWidgetH12BC), background="#FF6600")
if (length(con[which(con[,1]=="cbWith Allels"),2]) > 0){
cbValue <- tclVar(con[which(con[,1]=="cbWith Allels"),2])
}else{
cbValue <- tclVar("0")
}
tkconfigure(cb,variable=cbValue)
tkgrid(tklabel(sf3,text="Analysis with more than one feature in data (aka HLA allels):", background="#FF6600"),cb, sticky="snew", columnspan=1)
graphicals <- tkframe(sf3,relief="groove",borderwidth=2)
graphicals2 <- tkframe(sf3,relief="groove",borderwidth=2)
tkgrid(graphicals, sticky="e")
tkgrid(graphicals2, sticky="snew")
#Co mutation graphics
heading2 <- tklabel(graphicals,text="Create graphics for n-tuple, one page per identifier", background="#FFCC99")
tkgrid(heading2, sticky="snew", columnspan=4)
button.widget_com <- tkbutton(graphicals,text="Select csv file",command=function()getcsvfile(cMlabelText1B, 5, 1))
cMlabelTextB <- tclVar("Result file from tuple analysis *:")
cMlabel1B <- tklabel(graphicals,text=tclvalue(cMlabelTextB))
tkconfigure(cMlabel1B,textvariable=cMlabelTextB)
cMlabelText1B <- tclVar("")
cMlabel2B <- tklabel(graphicals,text=tclvalue(cMlabelText1B))
tkconfigure(cMlabel2B,textvariable=cMlabelText1B)
tkgrid(cMlabel1B, cMlabel2B, button.widget_com)
cMlabelTextE <- tclVar("Significance level *:")
cMlabel1E <- tklabel(graphicals,text=tclvalue(cMlabelTextE))
if (length(con[which(con[,1]=="cMlevel for significance"),2]) > 0){
cMtextEntryE <- tclVar(con[which(con[,1]=="cMlevel for significance"),2])
}else{
cMtextEntryE <- tclVar("")
}
cMtextEntryWidgetE <- tkentry(graphicals,textvariable=cMtextEntryE)
tkgrid(cMlabel1E, cMtextEntryWidgetE)
OK.but22 <- tkbutton(graphicals, foreground = "red",text="Start",command=function()calculate_co_mut_graphics(cbVal2 <- as.character(tclvalue(cbValue)), tbn2, cMtextEntryE))
tkgrid(OK.but22)
###set left:
tkgrid.configure(cMlabel1B, sticky="w")
tkgrid.configure(cMlabel1E, sticky="w")
tkgrid.configure(cMlabel2B, column=2, sticky="w")
tkgrid.configure(cMtextEntryWidgetE, column=2)
tkgrid.configure(button.widget_com, column=3, sticky="e")
tkgrid.configure(OK.but22, column=3, sticky="e")
#double co mutation graphics
heading4 <- tklabel(graphicals2,text="Create tartan plot", background="#FFCC99")
tkgrid(heading4, sticky="snew", columnspan=4)
Tbutton.widget_com <- tkbutton(graphicals2,text="Select csv file",command=function()getcsvfile(TcMlabelText1B, 9, 1))
Tbutton.widget_com2 <- tkbutton(graphicals2,text="Select csv file",command=function()getcsvfile(TcMlabelText1B2, 9, 2))
Tbutton.widget_com3 <- tkbutton(graphicals2,text="Select csv file",command=function()getcsvfile(TcMlabelText1B3, 9, 3))
TcMlabelTextB <- tclVar("1st result from n-tuple vs. feature(s) *:")
TcMlabel1B <- tklabel(graphicals2,text=tclvalue(TcMlabelTextB))
tkconfigure(TcMlabel1B,textvariable=TcMlabelTextB)
TcMlabelText1B <- tclVar("")
TcMlabel2B <- tklabel(graphicals2,text=tclvalue(TcMlabelText1B))
tkconfigure(TcMlabel2B,textvariable=TcMlabelText1B)
tkgrid(TcMlabel1B, TcMlabel2B, Tbutton.widget_com)
TcMlabelTextB2 <- tclVar("2nd result from n-tuple vs. feature(s) *:")
TcMlabel1B2 <- tklabel(graphicals2,text=tclvalue(TcMlabelTextB2))
tkconfigure(TcMlabel1B2,textvariable=TcMlabelTextB2)
TcMlabelText1B2 <- tclVar("")
TcMlabel2B2 <- tklabel(graphicals2,text=tclvalue(TcMlabelText1B2))
tkconfigure(TcMlabel2B2,textvariable=TcMlabelText1B2)
tkgrid(TcMlabel1B2, TcMlabel2B2, Tbutton.widget_com2)
TcMlabelTextB3 <- tclVar("Optional: Distance matrix:")
TcMlabel1B3 <- tklabel(graphicals2,text=tclvalue(TcMlabelTextB3))
tkconfigure(TcMlabel1B3,textvariable=TcMlabelTextB3)
TcMlabelText1B3 <- tclVar("")
TcMlabel2B3 <- tklabel(graphicals2,text=tclvalue(TcMlabelText1B3))
tkconfigure(TcMlabel2B3,textvariable=TcMlabelText1B3)
tkgrid(TcMlabel1B3, TcMlabel2B3, Tbutton.widget_com3)
TcMlabelTextE <- tclVar("Optical space between blocks *:")
TcMlabel1E <- tklabel(graphicals2,text=tclvalue(TcMlabelTextE))
if (length(con[which(con[,1]=="space between blocks"),2]) > 0){
TcMtextEntryE <- tclVar(con[which(con[,1]=="space between blocks"),2])
}else{
TcMtextEntryE <- tclVar("")
}
TcMtextEntryWidgetE <- tkentry(graphicals2,textvariable=TcMtextEntryE)
tkgrid(TcMlabel1E, TcMtextEntryWidgetE)
TcMlabelTextE1 <- tclVar("Colors of the plot *:")
TcMlabel1E1 <- tklabel(graphicals2,text=tclvalue(TcMlabelTextE1))
if (length(con[which(con[,1]=="colors of the plot"),2]) > 0){
TcMtextEntryE1 <- tclVar(con[which(con[,1]=="colors of the plot"),2])
}else{
TcMtextEntryE1 <- tclVar("")
}
TcMtextEntryWidgetE1 <- tkentry(graphicals2,textvariable=TcMtextEntryE1)
tkgrid(TcMlabel1E1, TcMtextEntryWidgetE1)
TcMlabelTextE2 <- tclVar("x/y positions of added labels *:")
TcMlabel1E2 <- tklabel(graphicals2,text=tclvalue(TcMlabelTextE2))
if (length(con[which(con[,1]=="name positions"),2]) > 0){
TcMtextEntryE2 <- tclVar(con[which(con[,1]=="name positions"),2])
}else{
TcMtextEntryE2 <- tclVar("")
}
TcMtextEntryWidgetE2 <- tkentry(graphicals2,textvariable=TcMtextEntryE2)
tkgrid(TcMlabel1E2, TcMtextEntryWidgetE2)
TcMlabelTextE3 <- tclVar("Labelcontent *:")
TcMlabel1E3 <- tklabel(graphicals2,text=tclvalue(TcMlabelTextE3))
if (length(con[which(con[,1]=="names"),2]) > 0){
TcMtextEntryE3 <- tclVar(con[which(con[,1]=="names"),2])
}else{
TcMtextEntryE3 <- tclVar("")
}
TcMtextEntryWidgetE3 <- tkentry(graphicals2,textvariable=TcMtextEntryE3)
tkgrid(TcMlabel1E3, TcMtextEntryWidgetE3)
TcMlabelTextE4 <- tclVar("Ticks: ")
TcMlabel1E4 <- tklabel(graphicals2,text=tclvalue(TcMlabelTextE4))
if (length(con[which(con[,1]=="ticks"),2]) > 0){
TcMtextEntryE4 <- tclVar(con[which(con[,1]=="ticks"),2])
}else{
TcMtextEntryE4 <- tclVar("")
}
TcMtextEntryWidgetE4 <- tkentry(graphicals2,textvariable=TcMtextEntryE4)
tkgrid(TcMlabel1E4, TcMtextEntryWidgetE4)
TcMlabelTextE5 <- tclVar("Column nr. of 1st seq. pos. in 1st file *:")
TcMlabel1E5 <- tklabel(graphicals2,text=tclvalue(TcMlabelTextE5))
if (length(con[which(con[,1]=="column of first position in first file"),2]) > 0){
TcMtextEntryE5 <- tclVar(con[which(con[,1]=="column of first position in first file"),2])
}else{
TcMtextEntryE5 <- tclVar("")
}
TcMtextEntryWidgetE5 <- tkentry(graphicals2,textvariable=TcMtextEntryE5)
tkgrid(TcMlabel1E5, TcMtextEntryWidgetE5)
TcMlabelTextE6 <- tclVar("Column nr. of 2nd seq. pos. in 1st file *:")
TcMlabel1E6 <- tklabel(graphicals2,text=tclvalue(TcMlabelTextE6))
if (length(con[which(con[,1]=="column of second position in first file"),2]) > 0){
TcMtextEntryE6 <- tclVar(con[which(con[,1]=="column of second position in first file"),2])
}else{
TcMtextEntryE6 <- tclVar("")
}
TcMtextEntryWidgetE6 <- tkentry(graphicals2,textvariable=TcMtextEntryE6)
tkgrid(TcMlabel1E6, TcMtextEntryWidgetE6)
TcMlabelTextE7 <- tclVar("Column nr. of p-values in 1st file *:")
TcMlabel1E7 <- tklabel(graphicals2,text=tclvalue(TcMlabelTextE7))
if (length(con[which(con[,1]=="column of values in first file"),2]) > 0){
TcMtextEntryE7 <- tclVar(con[which(con[,1]=="column of values in first file"),2])
}else{
TcMtextEntryE7 <- tclVar("")
}
TcMtextEntryWidgetE7 <- tkentry(graphicals2,textvariable=TcMtextEntryE7)
tkgrid(TcMlabel1E7, TcMtextEntryWidgetE7)
TcMlabelTextE8 <- tclVar("Column nr. of 1st seq. pos. in 2nd file *:")
TcMlabel1E8 <- tklabel(graphicals2,text=tclvalue(TcMlabelTextE8))
if (length(con[which(con[,1]=="column of first position in second file"),2]) > 0){
TcMtextEntryE8 <- tclVar(con[which(con[,1]=="column of first position in second file"),2])
}else{
TcMtextEntryE8 <- tclVar("")
}
TcMtextEntryWidgetE8 <- tkentry(graphicals2,textvariable=TcMtextEntryE8)
tkgrid(TcMlabel1E8, TcMtextEntryWidgetE8)
TcMlabelTextE9 <- tclVar("Column nr. of 2nd seq. pos. in 2nd file *:")
TcMlabel1E9 <- tklabel(graphicals2,text=tclvalue(TcMlabelTextE9))
if (length(con[which(con[,1]=="column of second position in second file"),2]) > 0){
TcMtextEntryE9 <- tclVar(con[which(con[,1]=="column of second position in second file"),2])
}else{
TcMtextEntryE9 <- tclVar("")
}
TcMtextEntryWidgetE9 <- tkentry(graphicals2,textvariable=TcMtextEntryE9)
tkgrid(TcMlabel1E9, TcMtextEntryWidgetE9)
TcMlabelTextE0 <- tclVar("Column nr. of p-values in 2nd file *:")
TcMlabel1E0 <- tklabel(graphicals2,text=tclvalue(TcMlabelTextE0))
if (length(con[which(con[,1]=="column of values in second file"),2]) > 0){
TcMtextEntryE0 <- tclVar(con[which(con[,1]=="column of values in second file"),2])
}else{
TcMtextEntryE0 <- tclVar("")
}
TcMtextEntryWidgetE0 <- tkentry(graphicals2,textvariable=TcMtextEntryE0)
tkgrid(TcMlabel1E0, TcMtextEntryWidgetE0)
TOK.but22 <- tkbutton(graphicals2, foreground = "red",text="Start",command=function()calculate_co_mut_graphics_both(tbn5, txt, TcMtextEntryE, TcMtextEntryE1, TcMtextEntryE2, TcMtextEntryE3, TcMtextEntryE4, TcMtextEntryE5, TcMtextEntryE6, TcMtextEntryE7, TcMtextEntryE8, TcMtextEntryE9, TcMtextEntryE0))
tkgrid(TOK.but22)
###set left:
tkgrid.configure(TcMlabel1B, sticky="w")
tkgrid.configure(TcMlabel1B2, sticky="w")
tkgrid.configure(TcMlabel1B3, sticky="w")
tkgrid.configure(TcMlabel1E, sticky="w")
tkgrid.configure(TcMlabel1E1, sticky="w")
tkgrid.configure(TcMlabel1E2, sticky="w")
tkgrid.configure(TcMlabel1E3, sticky="w")
tkgrid.configure(TcMlabel1E4, sticky="w")
tkgrid.configure(TcMlabel1E5, sticky="w")
tkgrid.configure(TcMlabel1E6, sticky="w")
tkgrid.configure(TcMlabel1E7, sticky="w")
tkgrid.configure(TcMlabel1E8, sticky="w")
tkgrid.configure(TcMlabel1E9, sticky="w")
tkgrid.configure(TcMlabel1E0, sticky="w")
tkgrid.configure(TcMlabel2B, column=2, sticky="w")
tkgrid.configure(TcMlabel2B2, column=2, sticky="w")
tkgrid.configure(TcMtextEntryWidgetE, column=2)
tkgrid.configure(TcMtextEntryWidgetE1, column=2)
tkgrid.configure(TcMtextEntryWidgetE2, column=2)
tkgrid.configure(TcMtextEntryWidgetE3, column=2)
tkgrid.configure(TcMtextEntryWidgetE4, column=2)
tkgrid.configure(TcMtextEntryWidgetE5, column=2)
tkgrid.configure(TcMtextEntryWidgetE6, column=2)
tkgrid.configure(TcMtextEntryWidgetE7, column=2)
tkgrid.configure(TcMtextEntryWidgetE8, column=2)
tkgrid.configure(TcMtextEntryWidgetE9, column=2)
tkgrid.configure(TcMtextEntryWidgetE0, column=2)
tkgrid.configure(Tbutton.widget_com, column=3, sticky="e")
tkgrid.configure(Tbutton.widget_com2, column=3, sticky="e")
tkgrid.configure(Tbutton.widget_com3, column=3, sticky="e")
tkgrid.configure(TOK.but22, column=3, sticky="e")
#--------------------------------------------------------------------------------------------------------------------------------
tkgrid.rowconfigure(otbn3,0,weight=1, minsize=100)
tkgrid.columnconfigure(otbn3,0,weight=10, minsize=100)
tkgrid.columnconfigure(otbn3,1,weight=3, minsize=100)
tbn3 <- ttkframe(otbn3)
helptbn3 <- ttkframe(otbn3)
tkgrid(tbn3, helptbn3, sticky="snew")
tkgrid.columnconfigure(tbn3,0,weight=10)
tkgrid.columnconfigure(helptbn3,0,weight=1)
scr5 <- tkscrollbar(tbn3, command=function(...)tkyview(txt5,...),bg='white')
txt5 <- tktext(tbn3,height=1,width=5,bg='grey')
xscr5 <- tkscrollbar(tbn3, command=function(...)tkxview(txt5,...),orient='horiz')
tkconfigure(txt5, yscrollcommand=function(...)tkset(scr5,...), xscrollcommand=function(...)tkset(xscr5,...), state="disabled")
tkpack(scr5,side='right',fill='y')
tkpack(txt5,expand='yes',fill='both')
tkpack(xscr5, side="bottom", fill="x")
sf3 <- tkcanvas(txt5, background="white")
tkwindow.create(txt5,'end', window=sf3)
# small manhattan
sMA <- tkframe(sf3,relief="groove",borderwidth=2)
tkgrid(sMA, sticky="e")
headingsMA <- tklabel(sMA,text="Small manhattan plot", background="#FFCC99")
tkgrid(headingsMA, sticky="snew", columnspan=5)
button.widget_epi1 <- tkbutton(sMA,text="Select csv file",command=function()getcsvfile(sMAlabelText1, 12, 1))
sMAlabelText <- tclVar("Result from assoc point *: ")
sMAlabel1 <- tklabel(sMA,text=tclvalue(sMAlabelText))
tkconfigure(sMAlabel1,textvariable=sMAlabelText)
sMAlabelText1 <- tclVar("")
sMAlabel2 <- tklabel(sMA,text=tclvalue(sMAlabelText1))
tkconfigure(sMAlabel2,textvariable=sMAlabelText1)
tkgrid(sMAlabel1, sMAlabel2, button.widget_epi1)
sMAlabelTextC <- tclVar("Feature *: ")
sMAlabel1C <- tklabel(sMA,text=tclvalue(sMAlabelTextC))
if (length(con[which(con[,1]=="Feat"),2]) > 0){
sMAtextEntryC <- tclVar(con[which(con[,1]=="Feat"),2])
}else{
sMAtextEntryC <- tclVar("")
}
sMAtextEntryWidgetC <- tkentry(sMA,textvariable=sMAtextEntryC)
tkgrid(sMAlabel1C, sMAtextEntryWidgetC)
cb0sMA <- tkcheckbutton(sMA)
if (length(con[which(con[,1]=="corrected"),2]) > 0){
cbValue_0sMA <- tclVar(con[which(con[,1]=="corrected"),2])
}else{
cbValue_0sMA <- tclVar("0")
}
tkconfigure(cb0sMA,variable=cbValue_0sMA)
tkgrid(tklabel(sMA,text="Use corrected values?"),cb0sMA, sticky="snew")
sMAlabelTextF <- tclVar("x-axis-breaks *: ")
sMAlabel1F <- tklabel(sMA,text=tclvalue(sMAlabelTextF))
if (length(con[which(con[,1]=="axis_breaks"),2]) > 0){
sMAtextEntryF <- tclVar(con[which(con[,1]=="axis_breaks"),2])
}else{
sMAtextEntryF <- tclVar("")
}
sMAtextEntryWidgetF <- tkentry(sMA,textvariable=sMAtextEntryF)
tkgrid(sMAlabel1F, sMAtextEntryWidgetF)
OK.butsMA <- tkbutton(sMA,text="Start", foreground = "red",command=function()small_manhattan(tbn3, sMAtextEntryC, cbValue_0sMA, sMAtextEntryF, txt))
tkgrid(OK.butsMA)
###set left:
tkgrid.configure(sMAlabel1, sticky="w")
tkgrid.configure(sMAlabel1C, sticky="w")
tkgrid.configure(sMAlabel1F, sticky="w")
tkgrid.configure(sMAlabel2, column=2, columnspan=2, sticky="w")
tkgrid.configure(sMAtextEntryWidgetC, column=2, columnspan=2)
tkgrid.configure(sMAtextEntryWidgetF, column=2, columnspan=2)
tkgrid.configure(cb0sMA, column=2, columnspan=6)
tkgrid.configure(OK.butsMA, column=4, sticky="e")
tkgrid.configure(button.widget_epi1, column=4, sticky="e")
#Get frequencies###-----------------------
gF <- tkframe(sf3,relief="groove",borderwidth=2)
tkgrid(gF, sticky="snew")
headinggf <- tklabel(gF,text="Get frequencys for epitopes", background="#FFCC99")
tkgrid(headinggf, sticky="snew", columnspan=9)
button.widget_epi1 <- tkbutton(gF,text="Select FASTA file",command=function()getFASTAfile(gFlabelText1, 11, 1))
gFlabelText <- tclVar("Sequence alignment to analyse *: ")
gFlabel1 <- tklabel(gF,text=tclvalue(gFlabelText))
tkconfigure(gFlabel1,textvariable=gFlabelText)
gFlabelText1 <- tclVar("")
gFlabel2 <- tklabel(gF,text=tclvalue(gFlabelText1))
tkconfigure(gFlabel2,textvariable=gFlabelText1)
tkgrid(gFlabel1, gFlabel2, button.widget_epi1)
button.widget_epi12 <- tkbutton(gF,text="Select FASTA file",command=function()getFASTAfile(gFlabelText12, 11, 2))
gFlabelText2 <- tclVar("Sequence consensus*: ")
gFlabel12 <- tklabel(gF,text=tclvalue(gFlabelText2))
tkconfigure(gFlabel12,textvariable=gFlabelText2)
gFlabelText12 <- tclVar("")
gFlabel22 <- tklabel(gF,text=tclvalue(gFlabelText12))
tkconfigure(gFlabel22,textvariable=gFlabelText12)
tkgrid(gFlabel12, gFlabel22, button.widget_epi12)
gFlabelTextC <- tclVar("Starting pos. of epitope in alignment *: ")
gFlabel1C <- tklabel(gF,text=tclvalue(gFlabelTextC))
if (length(con[which(con[,1]=="Epi start"),2]) > 0){
gFtextEntryC <- tclVar(con[which(con[,1]=="Epi start"),2])
}else{
gFtextEntryC <- tclVar("")
}
gFtextEntryWidgetC <- tkentry(gF,textvariable=gFtextEntryC)
tkgrid(gFlabel1C, gFtextEntryWidgetC)
gFlabelTextD <- tclVar("Ending pos. of epitope in alignment *: ")
gFlabel1D <- tklabel(gF,text=tclvalue(gFlabelTextD))
if (length(con[which(con[,1]=="Epi end"),2]) > 0){
gFtextEntryD <- tclVar(con[which(con[,1]=="Epi end"),2])
}else{
gFtextEntryD <- tclVar("")
}
gFtextEntryWidgetD <- tkentry(gF,textvariable=gFtextEntryD)
tkgrid(gFlabel1D, gFtextEntryWidgetD)
gFlabelTextF <- tclVar("Minimal number of members *: ")
gFlabel1F <- tklabel(gF,text=tclvalue(gFlabelTextF))
if (length(con[which(con[,1]=="Number of patients threshold"),2]) > 0){
gFtextEntryF <- tclVar(con[which(con[,1]=="Number of patients threshold"),2])
}else{
gFtextEntryF <- tclVar("")
}
gFtextEntryWidgetF <- tkentry(gF,textvariable=gFtextEntryF)
tkgrid(gFlabel1F, gFtextEntryWidgetF)
gFlabelTextH <- tclVar("Position of feature A *: ")
gFlabel1H <- tklabel(gF,text=tclvalue(gFlabelTextH))
if (length(con[which(con[,1]=="gfgF_HLA-A1"),2]) > 0){
gFtextEntryH <- tclVar(con[which(con[,1]=="gF_HLA-A1"),2])
}else{
gFtextEntryH <- tclVar("")
}
gFtextEntryWidgetH <- tkentry(gF,width=3,textvariable=gFtextEntryH)
gFlabelTextH1 <- tclVar("-")
gFlabel1H1 <- tklabel(gF,text=tclvalue(gFlabelTextH1))
if (length(con[which(con[,1]=="gF_HLA-A2"),2]) > 0){
gFtextEntryH1 <- tclVar(con[which(con[,1]=="gF_HLA-A2"),2])
}else{
gFtextEntryH1 <- tclVar("")
}
gFtextEntryWidgetH1 <- tkentry(gF,width=3,textvariable=gFtextEntryH1)
if (length(con[which(con[,1]=="gF_HLA-A3"),2]) > 0){
gFtextEntryH2 <- tclVar(con[which(con[,1]=="gF_HLA-A3"),2])
}else{
gFtextEntryH2 <- tclVar("")
}
gFtextEntryWidgetH2 <- tkentry(gF,width=3,textvariable=gFtextEntryH2)
gFlabelTextH12 <- tclVar("-")
gFlabel1H12 <- tklabel(gF,text=tclvalue(gFlabelTextH12))
if (length(con[which(con[,1]=="gF_HLA-A4"),2]) > 0){
gFtextEntryH12 <- tclVar(con[which(con[,1]=="gF_HLA-A4"),2])
}else{
gFtextEntryH12 <- tclVar("")
}
gFtextEntryWidgetH12 <- tkentry(gF,width=3,textvariable=gFtextEntryH12)
tkgrid(gFlabel1H, gFtextEntryWidgetH, gFlabel1H1, gFtextEntryWidgetH1, gFtextEntryWidgetH2, gFlabel1H12, gFtextEntryWidgetH12)
gFlabelTextHB <- tclVar("Position of feature B *: ")
gFlabel1HB <- tklabel(gF,text=tclvalue(gFlabelTextHB))
if (length(con[which(con[,1]=="gF_HLA-B1"),2]) > 0){
gFtextEntryHB <- tclVar(con[which(con[,1]=="gF_HLA-B1"),2])
}else{
gFtextEntryHB <- tclVar("")
}
gFtextEntryWidgetHB <- tkentry(gF,width=3,textvariable=gFtextEntryHB)
gFlabelTextH1B <- tclVar("-")
gFlabel1H1B <- tklabel(gF,text=tclvalue(gFlabelTextH1B))
if (length(con[which(con[,1]=="gF_HLA-B2"),2]) > 0){
gFtextEntryH1B <- tclVar(con[which(con[,1]=="gF_HLA-B2"),2])
}else{
gFtextEntryH1B <- tclVar("")
}
gFtextEntryWidgetH1B <- tkentry(gF,width=3,textvariable=gFtextEntryH1B)
if (length(con[which(con[,1]=="gF_HLA-B3"),2]) > 0){
gFtextEntryH2B <- tclVar(con[which(con[,1]=="gF_HLA-B3"),2])
}else{
gFtextEntryH2B <- tclVar("")
}
gFtextEntryWidgetH2B <- tkentry(gF,width=3,textvariable=gFtextEntryH2B)
gFlabelTextH12B <- tclVar("-")
gFlabel1H12B <- tklabel(gF,text=tclvalue(gFlabelTextH12B))
if (length(con[which(con[,1]=="gF_HLA-B4"),2]) > 0){
gFtextEntryH12B <- tclVar(con[which(con[,1]=="gF_HLA-B4"),2])
}else{
gFtextEntryH12B <- tclVar("")
}
gFtextEntryWidgetH12B <- tkentry(gF,width=3,textvariable=gFtextEntryH12B)
tkgrid(gFlabel1HB, gFtextEntryWidgetHB, gFlabel1H1B, gFtextEntryWidgetH1B, gFtextEntryWidgetH2B, gFlabel1H12B, gFtextEntryWidgetH12B)
OK.but10 <- tkbutton(gF,text="Start", foreground = "red",command=function()get_freqs(tbn3, gFtextEntryC, gFtextEntryD, gFtextEntryF, gFtextEntryH, gFtextEntryH1, gFtextEntryH2, gFtextEntryH12, gFtextEntryHB, gFtextEntryH1B, gFtextEntryH2B, gFtextEntryH12B, txt))
tkgrid(OK.but10)
###set left:
tkgrid.configure(gFlabel1, sticky="w")
tkgrid.configure(gFlabel12, sticky="w")
tkgrid.configure(gFlabel1C, sticky="w")
tkgrid.configure(gFlabel1D, sticky="w")
tkgrid.configure(gFlabel1F, sticky="w")
tkgrid.configure(gFlabel1H, sticky="w")
tkgrid.configure(gFlabel1HB, sticky="w")
tkgrid.configure(gFlabel2, column=2, columnspan=6, sticky="w")
tkgrid.configure(gFlabel22, column=2, columnspan=6, sticky="w")
tkgrid.configure(gFtextEntryWidgetC, column=2, columnspan=6)
tkgrid.configure(gFtextEntryWidgetD, column=2, columnspan=6)
tkgrid.configure(gFtextEntryWidgetF, column=2, columnspan=6)
tkgrid.configure(button.widget_epi1, column=8, sticky="e")
tkgrid.configure(button.widget_epi12, column=8, sticky="e")
tkgrid.configure(OK.but10, column=8, sticky="e")
tkgrid.configure(gFtextEntryWidgetH, column=2)
tkgrid.configure(gFlabel1H1, column=3)
tkgrid.configure(gFtextEntryWidgetH1, column=4)
tkgrid.configure(gFtextEntryWidgetH2, column=5)
tkgrid.configure(gFlabel1H12, column=6)
tkgrid.configure(gFtextEntryWidgetH12, column=7)
tkgrid.configure(gFtextEntryWidgetHB, column=2)
tkgrid.configure(gFlabel1H1B, column=3)
tkgrid.configure(gFtextEntryWidgetH1B, column=4)
tkgrid.configure(gFtextEntryWidgetH2B, column=5)
tkgrid.configure(gFlabel1H12B, column=6)
tkgrid.configure(gFtextEntryWidgetH12B, column=7)
#----------------------------------------------------------------
qv <- tkframe(sf3,relief="groove",borderwidth=2)
tkgrid(qv, sticky="e")
heading4 <- tklabel(qv,text="Calculate q-values from p-values", background="#FFCC99")
tkgrid(heading4, sticky="snew", columnspan=4)
button.widget_q <- tkbutton(qv,text="Select csv file",command=function()getcsvfile(qVlabelText1, 3, 1))
qVlabelText <- tclVar("csv file *:")
qVlabel1 <- tklabel(qv,text=tclvalue(qVlabelText))
tkconfigure(qVlabel1,textvariable=qVlabelText)
qVlabelText1 <- tclVar("")
qVlabel2 <- tklabel(qv,text=tclvalue(qVlabelText1))
tkconfigure(qVlabel2,textvariable=qVlabelText1)
tkgrid(qVlabel1, qVlabel2, button.widget_q)
OK.but3 <- tkbutton(qv,text="Start", foreground = "red",command=function()calculate_q_value(tbn3, txt))
tkgrid(OK.but3)
###set left:
tkgrid.configure(qVlabel1, sticky="w")
tkgrid.configure(qVlabel2, column=2, sticky="w")
tkgrid.configure(button.widget_q, column=3, sticky="e")
tkgrid.configure(OK.but3, column=3, sticky="e")
#---------------------------------------------------------
epa <- tkframe(sf3,relief="groove",borderwidth=2)
tkgrid(epa, sticky="e")
heading <- tklabel(epa,text="Combine results of point and tuple mutations", background="#FFCC99")
tkgrid(heading, sticky="snew", columnspan=4)
button.widget_epa1 <- tkbutton(epa,text="Select FASTA file",command=function()getFASTAfile(pEFlabelText1, 4, 1))
pEFlabelText <- tclVar("Sequence alignment to analyse *:")
pEFlabel1 <- tklabel(epa,text=tclvalue(pEFlabelText))
tkconfigure(pEFlabel1,textvariable=pEFlabelText)
pEFlabelText1 <- tclVar("")
pEFlabel2 <- tklabel(epa,text=tclvalue(pEFlabelText1))
tkconfigure(pEFlabel2,textvariable=pEFlabelText1)
tkgrid(pEFlabel1, pEFlabel2, button.widget_epa1)
button.widget_epa2 <- tkbutton(epa,text="Select csv file",command=function()getcsvfile(pEFlabelText1A, 4, 2))
pEFlabelTextA <- tclVar("Result file from point mutations *:")
pEFlabel1A <- tklabel(epa,text=tclvalue(pEFlabelTextA))
tkconfigure(pEFlabel1A,textvariable=pEFlabelTextA)
pEFlabelText1A <- tclVar("")
pEFlabel2A <- tklabel(epa,text=tclvalue(pEFlabelText1A))
tkconfigure(pEFlabel2A,textvariable=pEFlabelText1A)
tkgrid(pEFlabel1A, pEFlabel2A, button.widget_epa2)
button.widget_epa3 <- tkbutton(epa,text="Select csv file",command=function()getcsvfile(pEFlabelText1B, 4, 3))
pEFlabelTextB <- tclVar("Result file from tuple mutations *:")
pEFlabel1B <- tklabel(epa,text=tclvalue(pEFlabelTextB))
tkconfigure(pEFlabel1B,textvariable=pEFlabelTextB)
pEFlabelText1B <- tclVar("")
pEFlabel2B <- tklabel(epa,text=tclvalue(pEFlabelText1B))
tkconfigure(pEFlabel2B,textvariable=pEFlabelText1B)
tkgrid(pEFlabel1B, pEFlabel2B, button.widget_epa3)
pElabelText2 <- tclVar("p-value *:")
pElabel2G <- tklabel(epa,text=tclvalue(pElabelText2))
if (length(con[which(con[,1]=="p-value addon"),2]) > 0){
textEntry_p.value <- tclVar(con[which(con[,1]=="p-value addon"),2])
}else{
textEntry_p.value <- tclVar("")
}
textEntry_Wp.value <- tkentry(epa,textvariable=textEntry_p.value)
tkgrid(pElabel2G, textEntry_Wp.value)
OK.bute2 <- tkbutton(epa,text="Start", foreground = "red",command=function()calculate_pos_epi_further(tbn3, textEntry_p.value, txt))
tkgrid(OK.bute2)
###set left:
tkgrid.configure(pEFlabel1, sticky="w")
tkgrid.configure(pEFlabel1A, sticky="w")
tkgrid.configure(pEFlabel1B, sticky="w")
tkgrid.configure(pElabel2G, sticky="w")
tkgrid.configure(pEFlabel2, column=2, sticky="w")
tkgrid.configure(pEFlabel2A, column=2, sticky="w")
tkgrid.configure(pEFlabel2B, column=2, sticky="w")
tkgrid.configure(textEntry_Wp.value, sticky="w")
tkgrid.configure(button.widget_epa1, column=3, sticky="e")
tkgrid.configure(button.widget_epa2, column=3, sticky="e")
tkgrid.configure(button.widget_epa3, column=3, sticky="e")
tkgrid.configure(OK.bute2, column=3, sticky="e")
#-----------------------------------------------------
#Founder elem
fe <- tkframe(sf3,relief="groove",borderwidth=2)
tkgrid(fe, sticky="e")
heading3 <- tklabel(fe,text="Founder effect finder", background="#FFCC99")
tkgrid(heading3, sticky="snew", columnspan=4)
button.widget_fe1 <- tkbutton(fe,text="Select FASTA file",command=function()getFASTAfile(felabelText1, 6, 1))
felabelText <- tclVar("Sequence alignment to analyse *:")
felabel1 <- tklabel(fe,text=tclvalue(felabelText))
tkconfigure(felabel1,textvariable=felabelText)
felabelText1 <- tclVar("")
felabel2 <- tklabel(fe,text=tclvalue(felabelText1))
tkconfigure(felabel2,textvariable=felabelText1)
tkgrid(felabel1, felabel2, button.widget_fe1)
button.widget_fe2 <- tkbutton(fe,text="Select csv file",command=function()getcsvfile(felabelText12, 6, 2))
felabelText2 <- tclVar("Result file from tuple mutations *:")
felabel12 <- tklabel(fe,text=tclvalue(felabelText2))
tkconfigure(felabel12,textvariable=felabelText2)
felabelText12 <- tclVar("")
felabel22 <- tklabel(fe,text=tclvalue(felabelText12))
tkconfigure(felabel22,textvariable=felabelText12)
tkgrid(felabel12, felabel22, button.widget_fe2)
button.widget_fe3 <- tkbutton(fe,text="Select nexus file",command=function()getnexusfile(felabelText13, 6, 3))
felabelText3 <- tclVar("Tree file *:")
felabel13 <- tklabel(fe,text=tclvalue(felabelText3))
tkconfigure(felabel13,textvariable=felabelText3)
felabelText13 <- tclVar("")
felabel23 <- tklabel(fe,text=tclvalue(felabelText13))
tkconfigure(felabel23,textvariable=felabelText13)
tkgrid(felabel13, felabel23, button.widget_fe3)
felabelTextE <- tclVar("Ratio in subtree *:")
felabel1E <- tklabel(fe,text=tclvalue(felabelTextE))
if (length(con[which(con[,1]=="Ratio in subtree"),2]) > 0){
fetextEntryE <- tclVar(con[which(con[,1]=="Ratio in subtree"),2])
}else{
fetextEntryE <- tclVar("")
}
fetextEntryWidgetE <- tkentry(fe,width=20,textvariable=fetextEntryE)
tkgrid(felabel1E, fetextEntryWidgetE)
OK.but62 <- tkbutton(fe,text="Start", foreground = "red",command=function()calculate_founder(tbn3, fetextEntryE, txt))
tkgrid(OK.but62)
###set left:
tkgrid.configure(felabel1, sticky="w")
tkgrid.configure(felabel12, sticky="w")
tkgrid.configure(felabel13, sticky="w")
tkgrid.configure(felabel1E, sticky="w")
tkgrid.configure(felabel2, column=2, sticky="w")
tkgrid.configure(felabel22, column=2, sticky="w")
tkgrid.configure(felabel23, column=2, sticky="w")
tkgrid.configure(fetextEntryWidgetE, column=2, sticky="w")
tkgrid.configure(button.widget_fe1, column=3, sticky="e")
tkgrid.configure(button.widget_fe2, column=3, sticky="e")
tkgrid.configure(button.widget_fe3, column=3, sticky="e")
tkgrid.configure(OK.but62, column=3, sticky="e")
#### Rewrite shared mutations----------------------------
rsm <- tkframe(sf3,relief="groove",borderwidth=2)
tkgrid(rsm, sticky="e")
heading3 <- tklabel(rsm,text="Rewrite tuple analysis result for tartan", background="#FFCC99")
tkgrid(heading3, sticky="snew", columnspan=4)
button.widget_rsm2 <- tkbutton(rsm,text="Select csv file",command=function()getcsvfile(rsmlabelText12, 10, 1))
rsmlabelText2 <- tclVar("Result file from tuple analysis *:")
rsmlabel12 <- tklabel(rsm,text=tclvalue(rsmlabelText2))
tkconfigure(rsmlabel12,textvariable=rsmlabelText2)
rsmlabelText12 <- tclVar("")
rsmlabel22 <- tklabel(rsm,text=tclvalue(rsmlabelText12))
tkconfigure(rsmlabel22,textvariable=rsmlabelText12)
tkgrid(rsmlabel12, rsmlabel22, button.widget_rsm2)
rsmlabelTextE5 <- tclVar("Column of 1st sequence position *:")
rsmlabel1E5 <- tklabel(rsm,text=tclvalue(rsmlabelTextE5))
if (length(con[which(con[,1]=="rw column of first position"),2]) > 0){
rsmtextEntryE5 <- tclVar(con[which(con[,1]=="rw column of first position"),2])
}else{
rsmtextEntryE5 <- tclVar("")
}
rsmtextEntryWidgetE5 <- tkentry(rsm,textvariable=rsmtextEntryE5)
tkgrid(rsmlabel1E5, rsmtextEntryWidgetE5)
rsmlabelTextE6 <- tclVar("Column of 2nd sequence position *:")
rsmlabel1E6 <- tklabel(rsm,text=tclvalue(rsmlabelTextE6))
if (length(con[which(con[,1]=="rw column of second position"),2]) > 0){
rsmtextEntryE6 <- tclVar(con[which(con[,1]=="rw column of second position"),2])
}else{
rsmtextEntryE6 <- tclVar("")
}
rsmtextEntryWidgetE6 <- tkentry(rsm,textvariable=rsmtextEntryE6)
tkgrid(rsmlabel1E6, rsmtextEntryWidgetE6)
rsmlabelTextE7 <- tclVar("Column of p-values *:")
rsmlabel1E7 <- tklabel(rsm,text=tclvalue(rsmlabelTextE7))
if (length(con[which(con[,1]=="rw column of values"),2]) > 0){
rsmtextEntryE7 <- tclVar(con[which(con[,1]=="rw column of values"),2])
}else{
rsmtextEntryE7 <- tclVar("")
}
rsmtextEntryWidgetE7 <- tkentry(rsm,textvariable=rsmtextEntryE7)
tkgrid(rsmlabel1E7, rsmtextEntryWidgetE7)
rsmlabelTextA <- tclVar("csv seperator *:")
rsmlabel1A <- tklabel(rsm,text=tclvalue(rsmlabelTextA))
if (length(con[which(con[,1]=="rw csv seperator"),2]) > 0){
rsmtextEntryA <- tclVar(con[which(con[,1]=="rw csv seperator"),2])
}else{
rsmtextEntryA <- tclVar("")
}
rsmtextEntryWidgetA <- tkentry(rsm,textvariable=rsmtextEntryA)
tkgrid(rsmlabel1A, rsmtextEntryWidgetA)
rsmlabelTextB <- tclVar("Significance value *:")
rsmlabel1B <- tklabel(rsm,text=tclvalue(rsmlabelTextB))
if (length(con[which(con[,1]=="rw threshold"),2]) > 0){
rsmtextEntryB <- tclVar(con[which(con[,1]=="rw threshold"),2])
}else{
rsmtextEntryB <- tclVar("")
}
rsmtextEntryWidgetB <- tkentry(rsm,textvariable=rsmtextEntryB)
tkgrid(rsmlabel1B, rsmtextEntryWidgetB)
OK.but72 <- tkbutton(rsm,text="Start", foreground = "red",command=function()rewrite_shared_mutations(tbn3, rsmtextEntryE5, rsmtextEntryE6, rsmtextEntryE7, rsmtextEntryA, rsmtextEntryB, txt))
tkgrid(OK.but72)
###set left:
tkgrid.configure(rsmlabel12, sticky="w")
tkgrid.configure(rsmlabel1E5, sticky="w")
tkgrid.configure(rsmlabel1E6, sticky="w")
tkgrid.configure(rsmlabel1E7, sticky="w")
tkgrid.configure(rsmlabel1A, sticky="w")
tkgrid.configure(rsmlabel1B, sticky="w")
tkgrid.configure(rsmlabel22, column=2, sticky="w")
tkgrid.configure(rsmtextEntryWidgetE5, column=2, sticky="w")
tkgrid.configure(rsmtextEntryWidgetE6, column=2, sticky="w")
tkgrid.configure(rsmtextEntryWidgetE7, column=2, sticky="w")
tkgrid.configure(rsmtextEntryWidgetA, column=2, sticky="w")
tkgrid.configure(rsmtextEntryWidgetB, column=2, sticky="w")
tkgrid.configure(button.widget_rsm2, column=3, sticky="e")
tkgrid.configure(OK.but72, column=3, sticky="e")
#--------------------------------------------------------HELP-TEXT-----------------------
txthelptbn <- tktext(helptbn,bg="white", font="Helvetica", width=20, wrap="word")
tkgrid(txthelptbn)
tkgrid.rowconfigure(txthelptbn,0,weight=1)
tkgrid.columnconfigure(txthelptbn,0,weight=1)
tkgrid.configure(txthelptbn,sticky='nswe')
helptbntext <- paste("##[Discover associations between point mutations and feature(s)]\n",
"\n",
"The input sequence alignment may consist either of DNA sequences (nucleotides) or amino acid sequences (amino acids). Undetermined nucleotides or amino acids have to be indicated by the letter 'X'.\n",
"\n",
"Sequences to analyze (FASTA)-MANDATORY: \n Sequence alignment file in FASTA format. Contains not only the sequences (as in usual FASTA files), but also feature information in the FASTA headers. See also tutorial.\n",
"\n",
"SeqFeatR can use either single features (ckeck 'One feature') or HLA-type like features. Single features are indicated in the FASTA headers as character strings (such as 'yes', 'no', '1', '2', '3', etc. - without the quotes) at the end of the FASTA headers, separated from the first part of the FASTA header by a semicolon. Alternatively, HLA-type-like features can be used in the FASTA headers, formatted in a block-structure. Here SeqFeatR has to be told where these blocks in the header are to be found.\n",
"\n",
"##[Visualize odds ratios and p-values]\n",
"\n",
"It is important to enter the correct columns. Please count them inside the csv result file from 'discover associations between point mutations and features'."
)
tryCatch({tkinsert(txthelptbn,"end",helptbntext)}, error = function(err) {})
tkconfigure(txthelptbn, state="disabled")
#-----
txthelptbn2 <- tktext(helptbn2,bg="white", font="Helvetica", width=20, wrap="word")
tkgrid(txthelptbn2)
tkgrid.rowconfigure(txthelptbn2,0,weight=1)
tkgrid.columnconfigure(txthelptbn2,0,weight=1)
tkgrid.configure(txthelptbn2,sticky='nswe')
helptbn2text <- paste("##[Discovering associations between mutation pairs and features]\n",
"\n",
"Find those position pairs above the chosen threshold which have an p-value above the chosen threshold.\n",
"You can choose whether to use feature specific analysis or not\n",
"\n",
"##[Discovering associations between mutation n-tuple and features]\n",
"\n",
"Find those position tuple(more than two members possible) which have an p-value above the chosen threshold from the analysis of point mutations and features."
)
tryCatch({tkinsert(txthelptbn2,"end",helptbn2text)}, error = function(err) {})
tkconfigure(txthelptbn2, state="disabled")
#-----
txthelptbn5 <- tktext(helptbn5,bg="white", font="Helvetica", width=20, wrap="word")
tkgrid(txthelptbn5)
tkgrid.rowconfigure(txthelptbn5,0,weight=1)
tkgrid.columnconfigure(txthelptbn5,0,weight=1)
tkgrid.configure(txthelptbn5,sticky='nswe')
helptbn5text <- paste("##[Tartan plot]\n",
"\n",
"For the tartan plot you can compare the results of two different pair mutation files. Be aware that for the additional ticks and notes in the plot you have to enter values which are inside the range of the sequence length which created this data.\n"
)
tryCatch({tkinsert(txthelptbn5,"end",helptbn5text)}, error = function(err) {})
tkconfigure(txthelptbn5, state="disabled")
#-----
txthelptbn3 <- tktext(helptbn3,bg="white", font="Helvetica", width=20, wrap="word")
tkgrid(txthelptbn3)
tkgrid.rowconfigure(txthelptbn3,0,weight=1)
tkgrid.columnconfigure(txthelptbn3,0,weight=1)
tkgrid.configure(txthelptbn3,sticky='nswe')
helptbn3text <- paste("##[Calculate q-values]\n",
"\n",
"The file for added q-value column has to have a column with \"p_value\" (not p-value!!) as heading.\n",
"\n",
"##[Founder effect finder]\n",
"\n",
"For analysis of a possible founder effect DON'T use a pair mutation result which differentiates between identifiers.\n"
)
tryCatch({tkinsert(txthelptbn3,"end",helptbn3text)}, error = function(err) {})
tkconfigure(txthelptbn3, state="disabled")
#--------------------------------------------------------TOOL-TIPS-----------------------
tk2tip(cb01, "If checked: FASTA file has to have nucleotides, if not amino acids.")
tk2tip(icb01, "If checked: data has only one feature (like tropism), if not two (like HLA types).")
tk2tip(button.widget_epi1, "Loads FASTA file with sequence alignment.")
tk2tip(button.widget_epi2, "Loads file with known epitopes. See example files.")
tk2tip(button.widget_epi3, "Loads file with known binding motifs. See example files.")
tk2tip(button.widget_epi4, "Load reference sequence for own position corrections, if you deleted position columns due to lots of gaps.")
tk2tip(textEntryWidgetC, "The minimum number of patients of one HLA type to consider in the calculation.")
tk2tip(textEntryWidgetD, "The optical level height of \"significant\" results in the graphical output.")
tk2tip(textEntryWidgetE, "The optical level height of \"star level\" results in the graphical output.")
tk2tip(OK.bute1, "Starts the calculation.")
tk2tip(textEntryWidgetH, "The position of the start of the first feature A allele in the description block of the FASTA file.")
tk2tip(textEntryWidgetH1, "The position of the end of the first feature A allele in the description block of the FASTA file.")
tk2tip(textEntryWidgetH2, "The position of the start of the second feature A allele in the description block of the FASTA file.")
tk2tip(textEntryWidgetH12,"The position of the end of the second feature A allele in the description block of the FASTA file.")
tk2tip(textEntryWidgetHB, "The position of the start of the first feature B allele in the description block of the FASTA file.")
tk2tip(textEntryWidgetH1B, "The position of the end of the first feature B allele in the description block of the FASTA file.")
tk2tip(textEntryWidgetH2B, "The position of the start of the second feature B allele in the description block of the FASTA file.")
tk2tip(textEntryWidgetH12B, "The position of the end of the second feature B allele in the description block of the FASTA file.")
tk2tip(cb0e, "Should a check for a phylogenetic bias be made?")
#tk2tip(textEntryWidgetKIB, "Which matrix should be applied for phylogenetic bias check?")
tk2tip(ddb, "Input can be: \"holm\", \"hochberg\", \"hommel\", \"bonferroni\", \"BH\", \"BY\", \"fdr\", \"none\" .")
tk2tip(textEntryWidgetH42B, "The size of the sliding window for graphical output. Must be greater than 1, ideally between 8-10 for class I HLA allels.")
tk2tip(Bbutton.widget_epi, "Loads csv file with results from 'Discover associations between point mutations and feature(s)'.")
tk2tip(BtextEntryWidgetA, "The separator used in the csv file.")
tk2tip(BtextEntryWidgetB, "The number of feature(s) in the csv file.")
tk2tip(BtextEntryWidgetC, "The first column with odds ratios.")
tk2tip(BtextEntryWidgetD, "The first column with p-values.")
tk2tip(BtextEntryWidgetE, "The column number with the name for the feature in the first row.")
tk2tip(BtextEntryWidgetF, "The number of columns for one identifier.")
tk2tip(BtextEntryWidgetG, "The first column of nucleotides/ amino acids (if existent).")
tk2tip(BtextEntryWidgetH, "The maximum value on the y-axis (minus and plus).")
tk2tip(BtextEntryWidgetI, "The main interval on the y-axis.")
tk2tip(BtextEntryWidgetJ, "If a color should be added, enter column number from csv file with values between 0 and 1.")
tk2tip(BtextEntryWidgetK, "Select with integer values if you want the first color further down.")
tk2tip(ddb2, "If p-values or OR should be plotted as height. P for p-value, OR for Odds ratios.")
tk2tip(BOK.bute2, "Starts the plot making.")
tk2tip(button.widget_epa1, "Loads FASTA file with sequences alignment.")
tk2tip(button.widget_epa2, "Loads file with results from 'Discover associations between point mutations and feature(s)'.")
tk2tip(button.widget_epa3, "Loads file with results from Tuple analysis.")
tk2tip(textEntry_Wp.value, "p-value for selecting results from Tuple analysis.")
tk2tip(OK.bute2, "Starts the calculation.")
#----
tk2tip(cb1, "Should analysis include different allels or compare to consensus?")
#----
tk2tip(cb, "Should analysis include different allels or compare to consensus?")
tk2tip(button.widget_co1, "Loads FASTA file with sequences alignment.")
tk2tip(button.widget_co2, "Loads file with consensus of sequences in FASTA file.")
tk2tip(cMtextEntryWidgetC, "The minimal number of patients which have the same feature type to be included in the analysis.")
tk2tip(cMtextEntryWidgetD, "p-value below which possible Tuple positions are included in the analysis.")
tk2tip(ddbc, "Input can be: \"holm\", \"hochberg\", \"hommel\", \"bonferroni\", \"BH\", \"BY\", \"fdr\", \"none\".")
tk2tip(cbm, "Should calculation be made with more than one core?")
tk2tip(OK.but21, "Starts the calculation.")
tk2tip(textEntryWidgetHC, "The position of the start of the first feature A allele in the description block of the FASTA file.")
tk2tip(textEntryWidgetH1C, "The position of the end of the first feature A allele in the description block of the FASTA file.")
tk2tip(textEntryWidgetH2C, "The position of the start of the second feature A allele in the description block of the FASTA file.")
tk2tip(textEntryWidgetH12C,"The position of the end of the second feature A allele in the description block of the FASTA file.")
tk2tip(textEntryWidgetHBC, "The position of the start of the first feature B allele in the description block of the FASTA file.")
tk2tip(textEntryWidgetH1BC, "The position of the end of the first feature B allele in the description block of the FASTA file.")
tk2tip(textEntryWidgetH2BC, "The position of the start of the second feature B allele in the description block of the FASTA file.")
tk2tip(textEntryWidgetH12BC, "The position of the end of the second feature B allele in the description block of the FASTA file.")
tk2tip(button.widget_com, "Loads Tuple results. Be careful with checking \"allels\" or \"no allels\".")
tk2tip(cMtextEntryWidgetE, "p-value for optical differentiation.")
tk2tip(OK.but22, "Starts the calculation.")
#----
tk2tip(Tbutton.widget_com, "The first file with two position columns and p-values (e.g. results from Tuple analysis).")
tk2tip(Tbutton.widget_com2, "The second file with two position columns and p-values (e.g. results from Tuple analysis).")
tk2tip(Tbutton.widget_com3, "A file with distance matrix values.")
tk2tip(TcMtextEntryWidgetE, "The optical space in pixle between the blocks.")
tk2tip(TcMtextEntryWidgetE1, "The colors of the plot, ranging from lowest to highest. Given as list: \"color1, color2, ...")
tk2tip(TcMtextEntryWidgetE2, "The positions for names for interesting positions. Given as list: \"pos1, pos2, ...\"")
tk2tip(TcMtextEntryWidgetE3, "The names for interesting positions. Given as list: \"name1, name2, ...\"")
tk2tip(TcMtextEntryWidgetE4, "The ticks on x and y axis.")
tk2tip(TcMtextEntryWidgetE5, "The column number of the first position in the first file.")
tk2tip(TcMtextEntryWidgetE6, "The column number of the second position in the first file.")
tk2tip(TcMtextEntryWidgetE7, "The column number of the value in the second file.")
tk2tip(TcMtextEntryWidgetE8, "The column number of the first position in the second file.")
tk2tip(TcMtextEntryWidgetE9, "The column number of the second position in the second file.")
tk2tip(TcMtextEntryWidgetE0, "The column number of the value in the first file.")
tk2tip(TOK.but22, "Starts the plotmaking")
#----
tk2tip(button.widget_sm1, "Loads FASTA file with sequences alignment.")
tk2tip(button.widget_sm2, "The result file from 'Discover associations between point mutations and feature(s)' or other file with positions and (p-)values.")
tk2tip(smtextEntryWidgetA, "The threshold below which a position should be taken for calculation.")
tk2tip(smtextEntryWidgetB, "The minimal number of tuple for position tuple.")
tk2tip(smtextEntryWidgetC, "The maximal number of tuple for position tuple.")
tk2tip(smtextEntryWidgetD, "The column number in which the feature is column name.")
tk2tip(smtextEntryWidgetE, "The column number of p-values for this feature.")
tk2tip(smtextEntryWidgetF, "The column number of amino acids/nucleotides for this feature.")
tk2tip(smtextEntryWidgetH, "The position of the start of the first feature A allele in the description block of the FASTA file.")
tk2tip(smtextEntryWidgetH1, "The position of the end of the first feature A allele in the description block of the FASTA file.")
tk2tip(smtextEntryWidgetH2, "The position of the start of the second feature A allele in the description block of the FASTA file.")
tk2tip(smtextEntryWidgetH12,"The position of the end of the second feature A allele in the description block of the FASTA file.")
tk2tip(smtextEntryWidgetHB, "The position of the start of the first feature B allele in the description block of the FASTA file.")
tk2tip(smtextEntryWidgetH1B, "The position of the end of the first feature B allele in the description block of the FASTA file.")
tk2tip(smtextEntryWidgetH2B, "The position of the start of the second feature B allele in the description block of the FASTA file.")
tk2tip(smtextEntryWidgetH12B, "The position of the end of the second feature B allele in the description block of the FASTA file.")
tk2tip(smtextEntryWidgetX , "The feature which should be analyzed (if there is a single one).")
tk2tip(OK.but4, "Starts the calculation.")
#----
tk2tip(button.widget_q, "Load file with \"p_value\" column.")
tk2tip(OK.but3, "Starts the calculation.")
tk2tip(button.widget_fe1, "Loads FASTA file with sequence alignment.")
tk2tip(button.widget_fe2, "Loads Tuple results. Not possible in combination with \"allels\".")
tk2tip(button.widget_fe3, "Loads tree file in nexus format.")
tk2tip(fetextEntryWidgetE, "Rate of co-mutation is in subtree vs is not in subtree.")
tk2tip(OK.but62, "Starts the calculation")
tk2tip(rsmtextEntryWidgetA, "The separator used in the csv file.")
tk2tip(rsmtextEntryWidgetB, "p-value for selecting intresting sequence positions.")
tk2tip(rsmtextEntryWidgetE5, "Column number with first sequence position.")
tk2tip(rsmtextEntryWidgetE6, "Column number with second sequence position.")
tk2tip(rsmtextEntryWidgetE7, "Column number with p-values.")
tk2tip(gFtextEntryWidgetC, "Starting position of the epitope in the alignment.")
tk2tip(gFtextEntryWidgetD, "Ending position of the epitope in the alignment.")
tk2tip(gFtextEntryWidgetF, "The minimum number of patients of one HLA type to consider in the calculation.")
tk2tip(gFtextEntryWidgetH, "The position of the start of the first feature A allele in the description block of the FASTA file.")
tk2tip(gFtextEntryWidgetH1, "The position of the end of the first feature A allele in the description block of the FASTA file.")
tk2tip(gFtextEntryWidgetH2, "The position of the start of the second feature A allele in the description block of the FASTA file.")
tk2tip(gFtextEntryWidgetH12, "The position of the end of the second feature A allele in the description block of the FASTA file.")
tk2tip(gFtextEntryWidgetHB, "The position of the start of the first feature B allele in the description block of the FASTA file.")
tk2tip(gFtextEntryWidgetH1B, "The position of the end of the first feature B allele in the description block of the FASTA file.")
tk2tip(gFtextEntryWidgetH2B, "The position of the start of the second feature B allele in the description block of the FASTA file.")
tk2tip(gFtextEntryWidgetH12B, "The position of the end of the second feature B allele in the description block of the FASTA file.")
tk2tip(sMAtextEntryWidgetC, "Feature for which the plot should be made.")
tk2tip(cb0sMA, "Should the corrected values be used?")
tk2tip(sMAtextEntryWidgetF, "The x-axis-breaks.")
#---------------------------------------------------------
tkbind(tt, "<Destroy>", function() tkdestroy(tn))
tkselect(tn, 0)
#-------------FOR CONFIG--------------------------------------------
z <- list()
z$cbValue01 <- list(cbValue01, "DNA")
z$cbValue_0e <- list(cbValue_0e, "Phylogenetic comparison")
z$cbValue_bayes_factor <- list(cbValue_bayes_factor, "Bayes Factor")
z$cbValue_K <- list(cbValue_K, "Constant Dirichlet precision parameter")
z$textEntryC <- list(textEntryC, "Number of patients threshold")
z$textEntryD <- list(textEntryD, "Height of horizontal bar")
z$textEntryE <- list(textEntryE, "Height of star level")
z$cbValue_0eG1 <- list(cbValue_0eG1, "pos_epi_plot")
z$cbValue_0eG1C <- list(cbValue_0eG1C, "has_C")
z$textEntryH <- list(textEntryH, "HLA-A1")
z$textEntryH1 <- list(textEntryH1, "HLA-A2")
z$textEntryH2 <- list(textEntryH2, "HLA-A3")
z$textEntryH12 <- list(textEntryH12, "HLA-A4")
z$textEntryHB <- list(textEntryHB, "HLA-B1")
z$textEntryH1B <- list(textEntryH1B, "HLA-B2")
z$textEntryH2B <- list(textEntryH2B, "HLA-B3")
z$textEntryH12B <- list(textEntryH12B, "HLA-B4")
z$textEntryHCC <- list(textEntryHCC, "HLA-C1")
z$textEntryH1CC <- list(textEntryH1CC, "HLA-C2")
z$textEntryH2CC <- list(textEntryH2CC, "HLA-C3")
z$textEntryH12CC <- list(textEntryH12CC, "HLA-C4")
z$textEntryIB <- list(textEntryIB, "p-value correction")
#z$textEntryKIB <- list(textEntryKIB, "Matrix for phylo")
z$dirichlet_precision_parameter_textEntry<- list(dirichlet_precision_parameter_textEntry, "Dirichlet precision parameter")
z$icbValue01 <- list(icbValue01, "One identifier")
z$textEntryH42B <- list(textEntryH42B, "window_size")
z$textEntry_p.value <- list(textEntry_p.value, "p-value addon")
z$BtextEntryA <- list(BtextEntryA, "csv seperator")
z$BtextEntryB <- list(BtextEntryB, "number of cases")
z$BtextEntryC <- list(BtextEntryC, "position of odds.ratio")
z$BtextEntryD <- list(BtextEntryD, "position of p.values")
z$BtextEntryE <- list(BtextEntryE, "name for the y-axis label")
z$BtextEntryF <- list(BtextEntryF, "frequency")
z$BtextEntryG <- list(BtextEntryG, "position of amino acid")
z$BtextEntryH <- list(BtextEntryH, "maximum value of y-axis")
z$BtextEntryI <- list(BtextEntryI, "intervall of y-axis")
z$BtextEntryJ <- list(BtextEntryJ, "add color information")
z$BtextEntryK <- list(BtextEntryK, "bias")
z$cMtextEntryC <- list(cMtextEntryC, "Number of patients threshold_cm")
z$cMtextEntryD <- list(cMtextEntryD, "level for significance")
z$cmtextEntryIB <- list(cmtextEntryIB, "cmp-value correction")
z$cbValuem <- list(cbValuem, "More than one core")
z$textEntryHC <- list(textEntryHC, "cmHLA-A1")
z$textEntryH1C <- list(textEntryH1C, "cmHLA-A2")
z$textEntryH2C <- list(textEntryH2C, "cmHLA-A3")
z$textEntryH12C <- list(textEntryH12C,"cmHLA-A4")
z$textEntryHBC <- list(textEntryHBC, "cmHLA-B1")
z$textEntryH1BC <- list(textEntryH1BC, "cmHLA-B2")
z$textEntryH2BC <- list(textEntryH2BC, "cmHLA-B3")
z$textEntryH12BC <- list(textEntryH12BC, "cmHLA-B4")
z$fetextEntryE <- list(fetextEntryE, "Ratio in subtree")
z$cMtextEntryE <- list(cMtextEntryE, "cMlevel for significance")
z$TcMtextEntryE <- list(TcMtextEntryE, "space between blocks")
z$TcMtextEntryE1 <- list(TcMtextEntryE1, "colors of the plot")
z$TcMtextEntryE2 <- list(TcMtextEntryE2, "name positions")
z$TcMtextEntryE3 <- list(TcMtextEntryE3, "names")
z$TcMtextEntryE4 <- list(TcMtextEntryE4, "ticks")
z$TcMtextEntryE5 <- list(TcMtextEntryE5, "column of first position in first file")
z$TcMtextEntryE6 <- list(TcMtextEntryE6, "column of second position in first file")
z$TcMtextEntryE7 <- list(TcMtextEntryE7, "column of values in first file")
z$TcMtextEntryE8 <- list(TcMtextEntryE8, "column of first position in second file")
z$TcMtextEntryE9 <- list(TcMtextEntryE9, "column of second position in second file")
z$TcMtextEntryE0 <- list(TcMtextEntryE0, "column of values in second file")
z$smtextEntryA <- list(smtextEntryA, "threshold")
z$smtextEntryB <- list(smtextEntryB, "min_number_of_ele_in_tupel")
z$smtextEntryC <- list(smtextEntryC, "max_number_of_ele_in_tupel")
z$cbValue_0sM <- list(cbValue_0sM, "column")
z$cbValue_0sM2 <- list(cbValue_0sM2, "column of position")
z$smtextEntryE <- list(smtextEntryE, "column of values")
z$smtextEntryF <- list(smtextEntryF, "column of aas")
z$smtextEntryH <- list(smtextEntryH, "smHLA-A1")
z$smtextEntryH1 <- list(smtextEntryH1, "smHLA-A2")
z$smtextEntryH2 <- list(smtextEntryH2, "smHLA-A3")
z$smtextEntryH12 <- list(smtextEntryH12,"smHLA-A4")
z$smtextEntryHB <- list(smtextEntryHB, "smHLA-B1")
z$smtextEntryH1B <- list(smtextEntryH1B, "smHLA-B2")
z$smtextEntryH2B <- list(smtextEntryH2B, "smHLA-B3")
z$smtextEntryH12B <- list(smtextEntryH12B, "smHLA-B4")
z$smtextEntryidet <- list(smtextEntryidet, "Identifier")
z$rsmtextEntryE5 <- list(rsmtextEntryE5, "rw column of first position")
z$rsmtextEntryE6 <- list(rsmtextEntryE6, "rw column of second position")
z$rsmtextEntryE7 <- list(rsmtextEntryE7, "rw column of values")
z$rsmtextEntryA <- list(rsmtextEntryA, "rw csv seperator")
z$rsmtextEntryB <- list(rsmtextEntryB, "rw threshold")
z$gFtextEntryC <- list(gFtextEntryC, "Epi start")
z$gFtextEntryD <- list(gFtextEntryD, "Epi end")
z$gFtextEntryF <- list(gFtextEntryF, "Number of patients threshold")
z$gFtextEntryH <- list(gFtextEntryH, "gFHLA-A1")
z$gFtextEntryH1 <- list(gFtextEntryH1, "gFHLA-A2")
z$gFtextEntryH2 <- list(gFtextEntryH2, "gFHLA-A3")
z$gFtextEntryH12 <- list(gFtextEntryH12, "gFHLA-A4")
z$gFtextEntryHB <- list(gFtextEntryHB, "gFHLA-B1")
z$gFtextEntryH1B <- list(gFtextEntryH1B, "gFHLA-B2")
z$gFtextEntryH2B <- list(gFtextEntryH2B, "gFHLA-B3")
z$gFtextEntryH12B <- list(gFtextEntryH12B, "gFHLA-B4")
z$sMAtextEntryC <- list(sMAtextEntryC, "Feat")
z$cbValue_0sMA <- list(cbValue_0sMA, "corrected")
z$sMAtextEntryF <- list(sMAtextEntryF, "axis_breaks")
.GlobalEnv[["z"]] <- z
#---------------------------------------------------------
},ex=function(){
SeqFeatR_GUI()
})
#SeqFeatR_GUI()
Try the SeqFeatR package in your browser
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SeqFeatR documentation built on May 2, 2019, 3:10 p.m.
R Package Documentation
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Defines functions get_label_right getcsvfile getFASTAfile getnexusfile check_phylo check_bayes_factor has_C_allel check_K check_offset check_allels check_dna check_ident generate_example_fasta generate_example_config generate_example_config_wo_HLA save_config read.config attach.config open_tutorial about calculate_pos_epi calculate_pos_epi_further create_sequence_graphic_G calculate_co_mut calculate_co_mut_graphics calculate_co_mut_graphics_both calculate_founder calculate_q_value shared_mutations rewrite_shared_mutations get_freqs small_manhattan
#R GUI written by Bettina Budeus, rokkaku-fight@gmx.de
#from 2012-07-27 to 2012-?-?
#GUI for scripts to better put data in it
#search for "change" for points where changes are possible
#please check before executing
rm(list = ls())
#libs
require(tcltk)
require(tcltk2)
require(widgetTools)
#----------------------------------------------------------------------------------------------------------------
#loaded objects
calculate_pos_epi_is_running <- FALSE
calculate_pos_epi_further_is_running <- FALSE
calculate_co_mut_is_running <- FALSE
calculate_q_value_is_running <- FALSE
calculate_co_mut_graphics_is_running <- FALSE
calculate_co_mut_graphics_both_is_running <- FALSE
calculate_founder_is_running <- FALSE
create_sequence_graphic_is_running <- FALSE
shared_mutations_is_running <- FALSE
rewrite_shared_mutations_is_running <- FALSE
get_freqs_is_running <- FALSE
small_manhattan_is_running <- FALSE
#----------------------------------------------------------------------------------------------------------------
#Error handling---------------------------------------------------------------------------------------------------
Require <- structure(function(
### checks if a package is available
pkg
### the package to check for
){
if (data.class(result<-try(find.package(pkg),TRUE))=="try-error") {
tkmessageBox(title="An error has occured!",message=paste("Cannot find package\"",pkg,"\". Please install it with install.packages(\"",pkg,"\")",sep=""),icon="error",type="ok")
return (FALSE)
}else{
require(pkg,character.only=TRUE)
return (TRUE)
}
### True if package is there, False if it is not
},ex=function(){
Require(tcltk)
})
#Helper-Functions for the program start---------------------------------------------------------------------------
get_label_right <- function(splitted){
length <- length(splitted[[1]])
if (length>1){
return (paste(splitted[[1]][2], "/../", splitted[[1]][length]))
}
else{
return (splitted[[1]][2])
}
}
getcsvfile <- function(labelT, funct, whichfile) {
loaded_files <- .GlobalEnv[["loaded_files"]]
name <- tclvalue(tkgetOpenFile(filetypes="{{csv Files} {.csv}} {{All files} *}"))
loaded_files[1, whichfile, funct] <- name
splitted <- strsplit(name, "/")
label <- get_label_right(splitted)
tclvalue(labelT) <- label
.GlobalEnv[["loaded_files"]] <- loaded_files
}
getFASTAfile <- function(labelT, funct, whichfile) {
loaded_files <- .GlobalEnv[["loaded_files"]]
name <- tclvalue(tkgetOpenFile(filetypes="{{FASTA Files} {.fasta}} {{All files} *}"))
loaded_files[1, whichfile, funct] <- name
splitted <- strsplit(name, "/")
label <- get_label_right(splitted)
tclvalue(labelT) <- label
.GlobalEnv[["loaded_files"]] <- loaded_files
}
getnexusfile <- function(labelT, funct, whichfile) {
loaded_files <- .GlobalEnv[["loaded_files"]]
name <- tclvalue(tkgetOpenFile(filetypes="{{nexus Files} {.nh}} {{All files} *}"))
loaded_files[1, whichfile, funct] <- name
splitted <- strsplit(name, "/")
label <- get_label_right(splitted)
tclvalue(labelT) <- label
.GlobalEnv[["loaded_files"]] <- loaded_files
}
check_phylo <- function(cbValue, textEntryWidgetKIB){
if (cbValue=="1"){
tkconfigure(textEntryWidgetKIB, state="normal")
}else {
tkconfigure(textEntryWidgetKIB, state="disabled")
}
}
check_bayes_factor <- function(cbValueBayes, cbValueconst, textEntryWidget){
if (cbValueBayes=="1" && cbValueconst=="0"){
tkconfigure(textEntryWidget, state="normal")
}else {
tkconfigure(textEntryWidget, state="disabled")
}
}
has_C_allel <- function(cbValuehasC, textEntryWidgetHCC, textEntryWidgetH1CC, textEntryWidgetH2CC, textEntryWidgetH12CC){
if (cbValuehasC=="1"){
tkconfigure(textEntryWidgetHCC, state="normal")
tkconfigure(textEntryWidgetH1CC, state="normal")
tkconfigure(textEntryWidgetH2CC, state="normal")
tkconfigure(textEntryWidgetH12CC, state="normal")
}else {
tkconfigure(textEntryWidgetHCC, state="disabled")
tkconfigure(textEntryWidgetH1CC, state="disabled")
tkconfigure(textEntryWidgetH2CC, state="disabled")
tkconfigure(textEntryWidgetH12CC, state="disabled")
}
}
check_K <- function(cbValueBayes, cbValueconst, textEntryWidget){
if (cbValueBayes=="1" && cbValueconst=="0"){
tkconfigure(textEntryWidget, state="normal")
}else {
tkconfigure(textEntryWidget, state="disabled")
}
}
check_offset <- function(cbvalues_off, textEntryWidget){
if (cbvalues_off=="1"){
tkconfigure(textEntryWidget, state="normal")
}else {
tkconfigure(textEntryWidget, state="disabled")
}
}
check_allels <- function(cbValue, cMtextEntryWidgetC, button.widget_co2, textEntryWidgetHC, textEntryWidgetH1C, textEntryWidgetH2C, textEntryWidgetH12C, textEntryWidgetHBC, textEntryWidgetH1BC, textEntryWidgetH2BC, textEntryWidgetH12BC) {
if (cbValue=="1"){
tkconfigure(cMtextEntryWidgetC, state="normal")
tkconfigure(button.widget_co2, state="disabled")
tkconfigure(textEntryWidgetHC, state="normal")
tkconfigure(textEntryWidgetH1C, state="normal")
tkconfigure(textEntryWidgetH2C, state="normal")
tkconfigure(textEntryWidgetH12C, state="normal")
tkconfigure(textEntryWidgetHBC, state="normal")
tkconfigure(textEntryWidgetH1BC, state="normal")
tkconfigure(textEntryWidgetH2BC, state="normal")
tkconfigure(textEntryWidgetH12BC, state="normal")
}else {
tkconfigure(cMtextEntryWidgetC, state="disabled")
tkconfigure(button.widget_co2, state="normal")
tkconfigure(textEntryWidgetHC, state="disabled")
tkconfigure(textEntryWidgetH1C, state="disabled")
tkconfigure(textEntryWidgetH2C, state="disabled")
tkconfigure(textEntryWidgetH12C, state="disabled")
tkconfigure(textEntryWidgetHBC, state="disabled")
tkconfigure(textEntryWidgetH1BC, state="disabled")
tkconfigure(textEntryWidgetH2BC, state="disabled")
tkconfigure(textEntryWidgetH12BC, state="disabled")
}
}
check_dna <- function(cbValue) {
if (cbValue=="1"){
}else {
}
}
check_ident <- function(cbValue, textEntryWidgetH, textEntryWidgetH1, textEntryWidgetH12, textEntryWidgetH2, textEntryWidgetHB, textEntryWidgetH1B, textEntryWidgetH12B, textEntryWidgetH2B, textEntryWidgetHC, textEntryWidgetH1C, textEntryWidgetH2C, textEntryWidgetH12C, textEntryWidgetHBC, textEntryWidgetH1BC, textEntryWidgetH2BC, textEntryWidgetH12BC, smtextEntryWidgetX, smtextEntryWidgetH, smtextEntryWidgetH1, smtextEntryWidgetH2, smtextEntryWidgetH12, smtextEntryWidgetHB, smtextEntryWidgetH1B, smtextEntryWidgetH2B, smtextEntryWidgetH12B) {
if (cbValue=="1"){
tkconfigure(textEntryWidgetH, state="disabled")
tkconfigure(textEntryWidgetH1, state="disabled")
tkconfigure(textEntryWidgetH12, state="disabled")
tkconfigure(textEntryWidgetH2, state="disabled")
tkconfigure(textEntryWidgetHB, state="disabled")
tkconfigure(textEntryWidgetH1B, state="disabled")
tkconfigure(textEntryWidgetH12B, state="disabled")
tkconfigure(textEntryWidgetH2B, state="disabled")
tkconfigure(textEntryWidgetHC, state="disabled")
tkconfigure(textEntryWidgetH1C, state="disabled")
tkconfigure(textEntryWidgetH2C, state="disabled")
tkconfigure(textEntryWidgetH12C, state="disabled")
tkconfigure(textEntryWidgetHBC, state="disabled")
tkconfigure(textEntryWidgetH1BC, state="disabled")
tkconfigure(textEntryWidgetH2BC, state="disabled")
tkconfigure(textEntryWidgetH12BC, state="disabled")
tkconfigure(smtextEntryWidgetX, state="normal")
tkconfigure(smtextEntryWidgetH, state="disabled")
tkconfigure(smtextEntryWidgetH1, state="disabled")
tkconfigure(smtextEntryWidgetH2, state="disabled")
tkconfigure(smtextEntryWidgetH12, state="disabled")
tkconfigure(smtextEntryWidgetHB, state="disabled")
tkconfigure(smtextEntryWidgetH1B, state="disabled")
tkconfigure(smtextEntryWidgetH2B, state="disabled")
tkconfigure(smtextEntryWidgetH12B, state="disabled")
}else {
tkconfigure(textEntryWidgetH, state="normal")
tkconfigure(textEntryWidgetH1, state="normal")
tkconfigure(textEntryWidgetH12, state="normal")
tkconfigure(textEntryWidgetH2, state="normal")
tkconfigure(textEntryWidgetHB, state="normal")
tkconfigure(textEntryWidgetH1B, state="normal")
tkconfigure(textEntryWidgetH12B, state="normal")
tkconfigure(textEntryWidgetH2B, state="normal")
tkconfigure(textEntryWidgetHC, state="normal")
tkconfigure(textEntryWidgetH1C, state="normal")
tkconfigure(textEntryWidgetH2C, state="normal")
tkconfigure(textEntryWidgetH12C, state="normal")
tkconfigure(textEntryWidgetHBC, state="normal")
tkconfigure(textEntryWidgetH1BC, state="normal")
tkconfigure(textEntryWidgetH2BC, state="normal")
tkconfigure(textEntryWidgetH12BC, state="normal")
tkconfigure(smtextEntryWidgetX, state="disabled")
tkconfigure(smtextEntryWidgetH, state="normal")
tkconfigure(smtextEntryWidgetH1, state="normal")
tkconfigure(smtextEntryWidgetH2, state="normal")
tkconfigure(smtextEntryWidgetH12, state="normal")
tkconfigure(smtextEntryWidgetHB, state="normal")
tkconfigure(smtextEntryWidgetH1B, state="normal")
tkconfigure(smtextEntryWidgetH2B, state="normal")
tkconfigure(smtextEntryWidgetH12B, state="normal")
}
}
generate_example_fasta <- function(){
sequences <- c("LPDIQGNENMGYQPSWIFCGMETNGSQCLEEMFHCCWINC", "MPDWNQKWGNDHLASINLD-WLKTIQQPGIEKHLRFYENW", "VPDASGKHGIIGMDVTSSMERRHGMVQLPWPAMVWGRPHW", "MPDVRGVGCARRDCLIVHRFCMPFNNQVYCKVWIVYWTYK", "QPDTPKITRKEATAIHKCGIHWQTNCQKLSTVHPFHHQVD", "SWDDFSDFTMVHQWYAQGTLGPYKAMQLKMIFQGVSIMEV", "IPDEPCYCCVKNKILTVEIGVHHAKSQVRRNIDNIRRKTE", "HFST-ICPYIWKMYFTWMGQKLVIQKVNGRTPPHCDECNQ", "SNFT-TTKLRDQHNLYPAGLQEIEHKVDHQILGIYGQIWY", "ETSTALRTQDQTFMLALRANYMVMLKVLDCISVKLFICWR", "DSSTMDAECSTLQRFIWWHAHYAWIRVAKKPYCLDCPYAV", "KKSTLGIARGIQRSHGWYWRQTHCVMVLTPSQHKMGEKSW", "ICSTELCGCLINWPPMQWIVFAHMDDVNDSQTNTCDMRSQ", "GPSTNARTMGGQDCAYMTHTLTKHIWVILAFDPIMIVHKP")
names <- c("P01_HLA_A01_00_B01_02_C22_01", "P02_HLA_A01_00_B01_02_C22_01", "P03_HLA_A01_02_B01_02_C22_01", "P04_HLA_A01_00_B01_02_C22_01", "P05_HLA_A01_00_B01_02_C22_01", "P06_HLA_A01_02_B01_02_C22_01", "P07_HLA_A01_02_B01_02_C22_01", "P08_HLA_A04_03_B04_03_C22_03", "P09_HLA_A04_03_B04_03_C22_01", "P10_HLA_A04_03_B04_03_C22_01", "P11_HLA_A04_03_B04_00_C22_03", "P12_HLA_A04_03_B04_03_C22_01", "P13_HLA_A04_03_B04_00_C22_01", "P14_HLA_A04_03_B04_03_C22_03")
aa_seqs <- AAStringSet(sequences)
names(aa_seqs) <- names
save_file <- tclvalue(tkgetSaveFile(initialfile = "Example_aa.fasta", filetypes = "{{Fasta Files} {.fasta}} {{All files} *}"))
writeXStringSet(aa_seqs, save_file)
}
generate_example_config <- function(){
config <- matrix(c("Number of patients threshold", "Height of horizontal bar", "Height of star level", "HLA-A1", "HLA-A2", "HLA-A3", "HLA-A4", "HLA-B1", "HLA-B2", "HLA-B3", "HLA-B4", "HLA-C1", "HLA-C2", "HLA-C3", "HLA-C4", "C allel", "p-value correction", "Phylogenetic comparison", "offset", "offset_value", "Bayes Factor", "Constant Dirichlet precision parameter", "Dirichlet precision parameter", "One identifier", "window_size", "DNA", "p-value addon", "csv seperator", "number of cases", "position of odds.ratio", "position of p.values", "name for the y-axis label", "frequency", "position of amino acid", "maximum value of y-axis", "intervall of y-axis", "add color information", "bias", "Number of patients threshold_cm", "level for significance", "More than one core", "cmHLA-A1", "cmHLA-A2", "cmHLA-A3", "cmHLA-A4", "cmHLA-B1", "cmHLA-B2", "cmHLA-B3", "cmHLA-B4", "cmp-value correction", "Ratio in subtree", "cMlevel for significance", "space between blocks", "colors of the plot", "name positions", "names", "ticks", "column of first position in first file", "column of second position in first file", "column of values in first file", "column of first position in second file", "column of second position in second file", "column of values in second file", "threshold", "min_number_of_ele_in_tupel", "max_number_of_ele_in_tupel", "column", "column of position", "column of values", "column of aas", "smHLA-A1", "smHLA-A2", "smHLA-A3", "smHLA-A4", "smHLA-B1", "smHLA-B2", "smHLA-B3", "smHLA-B4", "Identifier", "With Allels", "cbWith Allels", "rw column of first position", "rw column of second position", "rw column of values", "rw csv seperator", "rw threshold", "pos_epi_plot", "Epi start", "Epi end", "Epitope Consensus", "gFHLA-A1", "gFHLA-A2", "gFHLA-A3", "gFHLA-A4", "gFHLA-B1", "gFHLA-B2", "gFHLA-B3", "gFHLA-B4", "Feat", "corrected", "axis_break", "1", "0.01", "0.5", "10", "11", "13", "14", "17", "18", "20", "21", "23", "24", "26", "27", "0", "bonferroni", "0", "0", "10", "0", "1", "20", "0", "9", "0", "0.01", ";", "8", "6", "2", "2", "7", "NULL", "4", "0.2", "0", "5","1", "0.01", "0", "10", "11", "13", "14", "17", "18", "20", "21", "bonferroni", "7", "0.01", "5", "wheat, darkblue, black, green", "1,3", "S, F", "1,5", "4", "5", "7", "2", "3", "4", "0.2", "2", "2", "9", "1", "9", "12", "10", "11", "13", "14", "17", "18", "20", "21", "X4", "0", "0", "3", "4", "10", "\\t", "0.1", "TRUE", "1", "8", "LPDIQGNE", "10", "11", "13", "14", "17", "18", "20", "21", "A2", "0", "1,20,40"), ncol=2)
save_file <- tclvalue(tkgetSaveFile(initialfile = "example_config.cfg", filetypes = "{{Config Files} {.cfg}} {{All files} *}"))
write.table(config, save_file, append = FALSE, quote = FALSE, sep = "=", eol = "\n", na = "NA", dec = ".", row.names = FALSE, col.names = FALSE, qmethod = c("escape", "double"), fileEncoding = "")
}
generate_example_config_wo_HLA <- function(){
config <- matrix(c("Number of patients threshold", "Height of horizontal bar", "Height of star level", "p-value correction", "Phylogenetic comparison", "offset", "offset_value", "Bayes Factor", "Constant Dirichlet precision parameter", "Dirichlet precision parameter", "One identifier", "window_size", "DNA", "p-value addon", "csv seperator", "number of cases", "position of odds.ratio", "position of p.values", "name for the y-axis label", "frequency", "position of amino acid", "maximum value of y-axis", "intervall of y-axis", "add color information", "bias", "Number of patients threshold_cm", "level for significance", "More than one core", "cmHLA-A1", "cmHLA-A2", "cmHLA-A3", "cmHLA-A4", "cmHLA-B1", "cmHLA-B2", "cmHLA-B3", "cmHLA-B4", "cmp-value correction", "Ratio in subtree", "cMlevel for significance", "space between blocks", "colors of the plot", "name positions", "names", "ticks", "column of first position in first file", "column of second position in first file", "column of values in first file", "column of first position in second file", "column of second position in second file", "column of values in second file", "threshold", "min_number_of_ele_in_tupel", "max_number_of_ele_in_tupel", "column", "column of position", "column of values", "column of aas", "smHLA-A1", "smHLA-A2", "smHLA-A3", "smHLA-A4", "smHLA-B1", "smHLA-B2", "smHLA-B3", "smHLA-B4", "Identifier", "With Allels", "cbWith Allels", "rw column of first position", "rw column of second position", "rw column of values", "rw csv seperator", "rw threshold", "pos_epi_plot", "Epi start", "Epi end", "Epitope Consensus", "Feat", "corrected", "axis_break", "1", "0.01", "0.5", "bonferroni", "0", "0", "10", "0", "1", "20", "0", "9", "0", "0.01", ";", "8", "6", "2", "2", "7", "NULL", "4", "0.2", "0", "5", "1", "0.01", "0", "10", "11", "13", "14", "17", "18", "20", "21", "bonferroni", "7", "0.01", "5", "wheat, darkblue, black, green", "1,3", "S, F", "1,5", "4", "5", "7", "2", "3", "4", "0.2", "2", "2", "9", "1", "9", "12", "10", "11", "13", "14", "17", "18", "20", "21", "X4", "0", "0", "3", "4", "10", "\\t", "0.1", "TRUE", "1", "8", "LPDIQGNE", "A2", "0", "1,20,40"), ncol=2)
save_file <- tclvalue(tkgetSaveFile(initialfile = "example_config.cfg", filetypes = "{{Config Files} {.cfg}} {{All files} *}"))
write.table(config, save_file, append = FALSE, quote = FALSE, sep = "=", eol = "\n", na = "NA", dec = ".", row.names = FALSE, col.names = FALSE, qmethod = c("escape", "double"), fileEncoding = "")
}
save_config <- function(z){
table <- c()
save_file <- tclvalue(tkgetSaveFile(initialfile = "user_config.cfg", filetypes = "{{Config Files} {.cfg}} {{All files} *}"))
for (i in 1:length(z)){
key <- z[[i]][[2]]
value <- tclvalue(z[[i]][[1]])
table <- rbind(table, c(key, value))
}
write.table(table, save_file, append = FALSE, quote = FALSE, sep = "=", eol = "\n", na = "NA", dec = ".", row.names = FALSE, col.names = FALSE, qmethod = c("escape", "double"), fileEncoding = "")
}
read.config <- function(config){
tryCatch({
key.val <- read.table(config, sep="=", col.names=c("key","value"), as.is=c(1,2))
return (key.val)
}, error = function(err) {tkmessageBox(title="Error",message=paste("No config file loaded. Standard parameters will be used!\n", err),icon="error",type="ok")})
}
attach.config <- function(config){
z <- .GlobalEnv[["z"]]
#print (z)
tryCatch({
con <- read.table(config, sep="=", col.names=c("key","value"), as.is=c(1,2))
#print (con)
for (i in 1:length(z)){
object <- z[[i]][[1]]
object_name <- z[[i]][[2]]
nopt <- con[which(con[,1]==object_name),2]
#print (object)
#print (tclvalue(object))
#print (nopt)
tclvalue(object) <- nopt
}
}, error = function(err) {tkmessageBox(title="Error",message=paste("Error in config file.\n", err),icon="error",type="ok")})
}
open_tutorial <- function(){
epi <- vignette("SeqFeatR")
if (length(epi) > 0){
print (epi)
}
}
about <- function(){
tryCatch({
ReturnVal <- tkmessageBox(title = "About SeqFeatR", message = paste("SeqFeatR Version ", packageVersion("SeqFeatR"), sep=""), icon = "info", type = "ok")
}, error = function(err) {tkmessageBox(title="Error",message=paste("SeqFeatR is not installed"),icon="error",type="ok")})
}
#Functions for the program start-------------------------------------------------------------------------------------------
calculate_pos_epi <- function(tbn, cbValue01, cbValue_0e, textEntryC, textEntryD, textEntryE, textEntryH, textEntryH1, textEntryH2, textEntryH12, textEntryHB, textEntryH1B, textEntryH2B, textEntryH12B, textEntryHCC, textEntryH1CC, textEntryH2CC, textEntryH12CC, cbValue_0eG1C, textEntryIB, txt, icbValue01, textEntryH42B, cbValue_0eG1, cbValue_bayes_factor, cbValue_K, dirichlet_precision_parameter_textEntry){
Require("Biostrings")
Require("plyr")
Require("plotrix")
loaded_files <- .GlobalEnv[["loaded_files"]]
tkconfigure(tbn,cursor="watch")
if (!calculate_pos_epi_is_running){
result <- c()
calculate_pos_epi_is_running <- TRUE
if (data.class(result<-try(find.package("SeqFeatR"),TRUE))=="try-error"){
source("assocpoint.R")
}
tryCatch({ep_wo_set_input_file_known_sequences(loaded_files[1,1,1])}, error = function(err) {tkmessageBox(title="An error has occured!",message="No sequence file",icon="error",type="ok")})
save_name_epi <- tclvalue(tkgetSaveFile(initialfile="epitope_results.pdf",filetypes="{{PDF Files} {.pdf}} {{All files} *}"))
if (!nchar(save_name_epi)){
tkmessageBox(message="No file was selected!")
}
save_name_epi_csv <- tclvalue(tkgetSaveFile(initialfile="epitope_results.csv",filetypes="{{csv Files} {.csv}} {{All files} *}"))
if (!nchar(save_name_epi_csv)){
tkmessageBox(message="No file was selected!")
}
if(as.numeric(tclvalue(textEntryH42B)) <=2){
print ("Beware! Window size smaller than 2! Will be set to 2")
tclvalue(textEntryH42B) <- 2
}
tryCatch({result <- assocpoint(loaded_files[1,1,1], loaded_files[1,2,1], loaded_files[1,3,1], save_name_epi, save_name_epi_csv, as.numeric(tclvalue(cbValue01)), as.numeric(tclvalue(textEntryC)), as.numeric(tclvalue(textEntryD)), as.numeric(tclvalue(textEntryE)), as.numeric(tclvalue(textEntryH)), as.numeric(tclvalue(textEntryH1)), as.numeric(tclvalue(textEntryH2)), as.numeric(tclvalue(textEntryH12)), as.numeric(tclvalue(textEntryHB)), as.numeric(tclvalue(textEntryH1B)), as.numeric(tclvalue(textEntryH2B)), as.numeric(tclvalue(textEntryH12B)), as.numeric(tclvalue(textEntryHCC)), as.numeric(tclvalue(textEntryH1CC)), as.numeric(tclvalue(textEntryH2CC)), as.numeric(tclvalue(textEntryH12CC)), as.logical(as.numeric(cbValue_0eG1C)), tclvalue(textEntryIB), as.logical(as.numeric(cbValue_bayes_factor)), as.logical(as.numeric(cbValue_K)), as.numeric(tclvalue(dirichlet_precision_parameter_textEntry)), as.numeric(tclvalue(cbValue_0e)), loaded_files[1,4,1], as.logical(as.numeric(icbValue01)), as.numeric(tclvalue(textEntryH42B)), as.logical(as.numeric(tclvalue(cbValue_0eG1))) )}, error = function(err) {tkmessageBox(title="An error has occured!",message=paste("No calculation done\n", err),icon="error",type="ok")})
old.option <- (getOption("width", default = NULL))
options(width=2000)
text <- paste(capture.output(print(result)),collapse="\n")
options(width=old.option)
tkconfigure(txt, state="normal")
tryCatch({tkinsert(txt,"end",text)}, error = function(err) {})
tkconfigure(txt, state="disabled")
calculate_pos_epi_is_running <- FALSE
}
tkconfigure(tbn,cursor="arrow")
}
calculate_pos_epi_further <- function(tbn, textEntry_p.value, txt){
Require("Biostrings")
loaded_files <- .GlobalEnv[["loaded_files"]]
tkconfigure(tbn,cursor="watch")
if (!calculate_pos_epi_further_is_running){
result_ef <- c()
calculate_pos_epi_further_is_running <- TRUE
if (data.class(result<-try(find.package("SeqFeatR"),TRUE))=="try-error"){
source("assocpointpair.R")
}
tryCatch({pos_epi_get_input_file_sequences(loaded_files[1,1,4])}, error = function(err) {tkmessageBox(title="An error has occured!",message="No sequence file",icon="error",type="ok")})
tryCatch({pos_epi_get_input_file_pos_epi(loaded_files[1,2,4])}, error = function(err) {tkmessageBox(title="An error has occured!",message="No possible epitope file",icon="error",type="ok")})
tryCatch({pos_epi_get_input_file_mut_core(loaded_files[1,3,4], as.numeric(tclvalue(textEntry_p.value)))}, error = function(err) {tkmessageBox(title="An error has occured!",message="No mutation core file",icon="error",type="ok")})
save_name_ef1 <- tclvalue(tkgetSaveFile(initialfile="co_mut_in_epitopes_result.csv",filetypes="{{csv Files} {.csv}} {{All files} *}"))
if (!nchar(save_name_ef1)){
tkmessageBox(message="No file was selected!")
}
save_name_ef2 <- tclvalue(tkgetSaveFile(initialfile="possible_compensatory_mutation.csv",filetypes="{{csv Files} {.csv}} {{All files} *}"))
if (!nchar(save_name_ef2)){
tkmessageBox(message="No file was selected!")
}
tryCatch({result_ef <- assocpointpair(loaded_files[1,1,4], loaded_files[1,2,4], loaded_files[1,3,4], as.numeric(tclvalue(textEntry_p.value)), save_name_ef1, save_name_ef2)}, error = function(err) {tkmessageBox(title="An error has occured!",message=paste("No calculation done\n", err),icon="error",type="ok")})
old.option <- (getOption("width", default = NULL))
options(width=2000)
text <- paste(capture.output(print (result_ef)),collapse="\n")
options(width=old.option)
tkconfigure(txt, state="normal")
tryCatch({tkinsert(txt,"end",text)}, error = function(err) {})
tkconfigure(txt, state="disabled")
calculate_pos_epi_further_is_running <- FALSE
}
tkconfigure(tbn,cursor="arrow")
}
create_sequence_graphic_G <- function(tbn, BtextEntryA, BtextEntryB, BtextEntryC, BtextEntryD, BtextEntryE, BtextEntryF, BtextEntryG, BtextEntryH, BtextEntryI, txt, BtextEntryJ, BtextEntryK, BtextEntryL){
Require("plotrix")
tkconfigure(tbn,cursor="watch")
loaded_files <- .GlobalEnv[["loaded_files"]]
if (as.character(tclvalue(BtextEntryA)) == "\\t"){
sep <- "\t"
}
else{
sep <- as.character(tclvalue(BtextEntryA))
}
if (!create_sequence_graphic_is_running){
result <- c()
create_sequence_graphic_is_running <- TRUE
if (data.class(result<-try(find.package("SeqFeatR"),TRUE))=="try-error"){
source("orPlot.R")
}
tryCatch({two_wo_set_input_file_known_sequences(loaded_files[1,1,7], sep)}, error = function(err) {tkmessageBox(title="An error has occured!",message="No result input file",icon="error",type="ok")})
save_name_two <- tclvalue(tkgetSaveFile(initialfile="final_graphic",filetypes="{{PDF Files} {.pdf}} {{All files} *}"))
if (!nchar(save_name_two)){
tkmessageBox(message="No file was selected!")
}
tryCatch({result <- orPlot(loaded_files[1,1,7], save_name_two, sep, as.numeric(tclvalue(BtextEntryB)), as.numeric(tclvalue(BtextEntryC)), as.numeric(tclvalue(BtextEntryD)), as.numeric(tclvalue(BtextEntryE)), as.numeric(tclvalue(BtextEntryF)), as.numeric(tclvalue(BtextEntryG)), as.numeric(tclvalue(BtextEntryH)), as.numeric(tclvalue(BtextEntryI)), as.numeric(tclvalue(BtextEntryJ)), as.numeric(tclvalue(BtextEntryK)), tclvalue(BtextEntryL))}, error = function(err) {tkmessageBox(title="An error has occured!",message=paste("No calculation done\n", err),icon="error",type="ok")})
old.option <- (getOption("width", default = NULL))
options(width=2000)
text <- paste(capture.output(print(result)),collapse="\n")
options(width=old.option)
tkconfigure(txt, state="normal")
tryCatch({tkinsert(txt,"end",text)}, error = function(err) {})
tkconfigure(txt, state="disabled")
create_sequence_graphic_is_running <- FALSE
}
tkconfigure(tbn,cursor="arrow")
}
calculate_co_mut <- function(allels, tbn2, txt, cMtextEntryC, cMtextEntryD, cmtextEntryIB, textEntryHC, textEntryH1C, textEntryH2C, textEntryH12C, textEntryHBC, textEntryH1BC, textEntryH2BC, textEntryH12BC, textEntryIB, cbValue01){
Require("Biostrings")
loaded_files <- .GlobalEnv[["loaded_files"]]
tkconfigure(tbn2,cursor="watch")
if (!calculate_co_mut_is_running){
result_co <- c()
calculate_co_mut_is_running <- TRUE
if (allels=="1"){
if (data.class(result<-try(find.package("SeqFeatR"),TRUE))=="try-error"){
source("assocpairfeat.R")
}
tryCatch({cm_get_input_file(loaded_files[1,1,2])}, error = function(err) {tkmessageBox(title="An error has occured!",message="No sequence file",icon="error",type="ok")})
save_name_co_mut <- tclvalue(tkgetSaveFile(initialfile="co_mutation_results.csv",filetypes="{{csv Files} {.csv}} {{All files} *}"))
if (!nchar(save_name_co_mut)){
tkmessageBox(message="No file was selected!")
}
tryCatch({result_co <- assocpairfeat(loaded_files[1,1,2], save_name_co_mut, as.numeric(tclvalue(cbValue01)), as.numeric(tclvalue(cMtextEntryC)), as.numeric(tclvalue(cMtextEntryD)), as.numeric(tclvalue(textEntryHC)), as.numeric(tclvalue(textEntryH1C)), as.numeric(tclvalue(textEntryH2C)), as.numeric(tclvalue(textEntryH12C)), as.numeric(tclvalue(textEntryHBC)), as.numeric(tclvalue(textEntryH1BC)), as.numeric(tclvalue(textEntryH2BC)), as.numeric(tclvalue(textEntryH12BC)), tclvalue(cmtextEntryIB))}, error = function(err) {tkmessageBox(title="An error has occured!",message="No comutation analysis done",icon="error",type="ok")})
}
if (allels=="0"){
if (data.class(result<-try(find.package("SeqFeatR"),TRUE))=="try-error"){
source("assocpair.R")
}
tryCatch({cm_wo_get_input_file_sequences(loaded_files[1,1,2])}, error = function(err) {tkmessageBox(title="An error has occured!",message="No sequence file",icon="error",type="ok")})
tryCatch({cm_wo_get_input_file_consensus(loaded_files[1,2,2])}, error = function(err) {tkmessageBox(title="An error has occured!",message="No consensus file",icon="error",type="ok")})
save_name_co_mut <- tclvalue(tkgetSaveFile(initialfile="co_mutation_results_wo_allels.csv",filetypes="{{csv Files} {.csv}} {{All files} *}"))
if (!nchar(save_name_co_mut)){
tkmessageBox(message="No file was selected!")
}
tryCatch({result_co <- assocpair(loaded_files[1,1,2], loaded_files[1,2,2], save_name_co_mut, as.numeric(tclvalue(cbValue01)), as.numeric(tclvalue(cMtextEntryD)), tclvalue(cmtextEntryIB))}, error = function(err) {tkmessageBox(title="An error has occured!",message=paste("No calculation done\n", err),icon="error",type="ok")})
}
old.option <- (getOption("width", default = NULL))
options(width=2000)
text <- paste(capture.output(print (result_co)),collapse="\n")
options(width=old.option)
tkconfigure(txt, state="normal")
tryCatch({tkinsert(txt,"end",text)}, error = function(err) {})
tkconfigure(txt, state="disabled")
calculate_co_mut_is_running <- FALSE
}
tkconfigure(tbn2,cursor="arrow")
}
calculate_co_mut_graphics <- function(allels, tbn2, cMtextEntryE){
Require("Biostrings")
loaded_files <- .GlobalEnv[["loaded_files"]]
tkconfigure(tbn2,cursor="watch")
if (!calculate_co_mut_graphics_is_running){
calculate_co_mut_graphics_is_running <- TRUE
if (allels=="1"){
if (data.class(result<-try(find.package("SeqFeatR"),TRUE))=="try-error"){
source("visualizepairfeat.R")
}
tryCatch({co_g_get_input_file(loaded_files[1,1,5])}, error = function(err) {tkmessageBox(title="An error has occured!",message="No input file",icon="error",type="ok")})
save_name <- tclvalue(tkgetSaveFile(initialfile="co_mut_g_results.pdf",filetypes="{{PDF Files} {.pdf}} {{All files} *}"))
if (!nchar(save_name)){
tkmessageBox(message="No file was selected!")
}
tryCatch({visualizepairfeat(loaded_files[1,1,5], save_name, as.numeric(tclvalue(cMtextEntryE)))}, error = function(err) {tkmessageBox(title="An error has occured!",message=paste("No calculation done\n", err),icon="error",type="ok")})
}
if (allels=="0"){
if (data.class(result<-try(find.package("SeqFeatR"),TRUE))=="try-error"){
source("visualizepair.R")
}
tryCatch({co_g_get_input_file_wo_allel(loaded_files[1,1,5])}, error = function(err) {tkmessageBox(title="An error has occured!",message="No input file",icon="error",type="ok")})
save_name <- tclvalue(tkgetSaveFile(initialfile="co_mut_g_results_wo_allels.pdf",filetypes="{{PDF Files} {.pdf}} {{All files} *}"))
if (!nchar(save_name)){
tkmessageBox(message="No file was selected!")
}
tryCatch({visualizepair(loaded_files[1,1,5], save_name, as.numeric(tclvalue(cMtextEntryE)))}, error = function(err) {tkmessageBox(title="An error has occured!",message=paste("No calculation done\n", err),icon="error",type="ok")})
}
calculate_co_mut_graphics_is_running <- FALSE
}
tkconfigure(tbn2,cursor="arrow")
}
calculate_co_mut_graphics_both <- function(tbn5, txt, TcMtextEntryE, TcMtextEntryE1, TcMtextEntryE2, TcMtextEntryE3, TcMtextEntryE4, TcMtextEntryE5, TcMtextEntryE6, TcMtextEntryE7, TcMtextEntryE8, TcMtextEntryE9, TcMtextEntryE0){
Require("Biostrings")
loaded_files <- .GlobalEnv[["loaded_files"]]
tkconfigure(tbn5,cursor="watch")
if (!calculate_co_mut_graphics_both_is_running){
calculate_co_mut_graphics_both_is_running <- TRUE
if (data.class(result<-try(find.package("SeqFeatR"),TRUE))=="try-error"){
source("tartan.R")
}
if (loaded_files[1,3,9] == "0"){
with_distance_matrix <- FALSE
} else{
with_distance_matrix <- TRUE
}
tryCatch({co_g_get_input_file_wo_allel(loaded_files[1,1,9])}, error = function(err) {tkmessageBox(title="An error has occured!",message="No input file",icon="error",type="ok")})
tryCatch({co_g_get_input_file2_wo_allel(loaded_files[1,2,9])}, error = function(err) {tkmessageBox(title="An error has occured!",message="No input file",icon="error",type="ok")})
tryCatch({co_g_get_distance_matrix(loaded_files[1,3,9], with_distance_matrix)}, error = function(err) {tkmessageBox(title="An error has occured!",message="No input file",icon="error",type="ok")})
save_name <- tclvalue(tkgetSaveFile(initialfile="co_mut_g_both_results.pdf",filetypes="{{PDF Files} {.pdf}} {{All files} *}"))
if (!nchar(save_name)){
tkmessageBox(message="No file was selected!")
}
list1 <- as.numeric(strsplit(as.character(tclvalue(TcMtextEntryE2)), ",")[[1]])
list2 <- as.numeric(strsplit(as.character(tclvalue(TcMtextEntryE4)), ",")[[1]])
tryCatch({result_tartan <- tartan(loaded_files[1,1,9], loaded_files[1,2,9], save_name, as.numeric(tclvalue(TcMtextEntryE)), strsplit(as.character(tclvalue(TcMtextEntryE1)), ",")[[1]], list1, strsplit(as.character(tclvalue(TcMtextEntryE3)), ",")[[1]], list2, as.numeric(tclvalue(TcMtextEntryE5)), as.numeric(tclvalue(TcMtextEntryE6)), as.numeric(tclvalue(TcMtextEntryE7)), as.numeric(tclvalue(TcMtextEntryE8)), as.numeric(tclvalue(TcMtextEntryE9)), as.numeric(tclvalue(TcMtextEntryE0)), with_distance_matrix, loaded_files[1,3,9] )}, error = function(err) {tkmessageBox(title="An error has occured!",message=paste("No calculation done\n", err),icon="error",type="ok")})
old.option <- (getOption("width", default = NULL))
options(width=2000)
text <- paste(capture.output(print (result_tartan)),collapse="\n")
options(width=old.option)
tkconfigure(txt, state="normal")
tryCatch({tkinsert(txt,"end",text)}, error = function(err) {})
tkconfigure(txt, state="disabled")
calculate_co_mut_graphics_both_is_running <- FALSE
}
tkconfigure(tbn5,cursor="arrow")
}
calculate_founder <- function(tbn2, fetextEntryE, txt){
Require("Biostrings")
Require("phangorn")
loaded_files <- .GlobalEnv[["loaded_files"]]
tkconfigure(tbn2,cursor="watch")
if (!calculate_founder_is_running){
result_fe <- c()
if (data.class(result<-try(find.package("SeqFeatR"),TRUE))=="try-error"){
source("foundereffectfinder.R")
}
calculate_founder_is_running <- TRUE
tryCatch({fe_wo_get_input_file_known_sequences(loaded_files[1,1,6])}, error = function(err) {tkmessageBox(title="An error has occured!",message="No input file",icon="error",type="ok")})
tryCatch({fe_wo_get_input_file_co_mut_results(loaded_files[1,2,6])}, error = function(err) {tkmessageBox(title="An error has occured!",message="No input file",icon="error",type="ok")})
tryCatch({fe_wo_get_input_file_tree(loaded_files[1,3,6])}, error = function(err) {tkmessageBox(title="An error has occured!",message="No input file",icon="error",type="ok")})
save_name_fe <- tclvalue(tkgetSaveFile(initialfile="co_mut_results_from_founder.csv",filetypes="{{csv Files} {.csv}} {{All files} *}"))
if (!nchar(save_name_fe)){
tkmessageBox(message="No file was selected!")
}
tryCatch({result_fe <- foundereffectfinder(loaded_files[1,1,6], loaded_files[1,2,6], loaded_files[1,3,6], save_name_fe, as.numeric(tclvalue(fetextEntryE)))}, error = function(err) {tkmessageBox(title="An error has occured!",message=paste("No calculation done\n", err),icon="error",type="ok")})
old.option <- (getOption("width", default = NULL))
options(width=2000)
text <- paste(capture.output(print (result_fe)),collapse="\n")
options(width=old.option)
tkconfigure(txt, state="normal")
tryCatch({tkinsert(txt,"end",text)}, error = function(err) {})
tkconfigure(txt, state="disabled")
calculate_founder_is_running <- FALSE
}
tkconfigure(tbn2,cursor="arrow")
}
calculate_q_value <- function(tbn3, txt){
Require("Biostrings")
Require("qvalue")
loaded_files <- .GlobalEnv[["loaded_files"]]
tkconfigure(tbn3,cursor="watch")
if (!calculate_q_value_is_running){
result_q <- c()
if (data.class(result<-try(find.package("SeqFeatR"),TRUE))=="try-error"){
source("q-values.R")
}
calculate_q_value_is_running <- TRUE
tryCatch({q_value_set_input_file(loaded_files[1,1,3])}, error = function(err) {tkmessageBox(title="An error has occured!",message="No input file",icon="error",type="ok")})
save_name_q <- tclvalue(tkgetSaveFile(initialfile="csv_with_q_values.csv",filetypes="{{csv Files} {.csv}} {{All files} *}"))
if (!nchar(save_name_q)){
tkmessageBox(message="No file was selected!")
}
tryCatch({result_q <- qvalues(loaded_files[1,1,3], save_name_q)}, error = function(err) {tkmessageBox(title="An error has occured!",message=paste("No calculation done\n", err),icon="error",type="ok")})
old.option <- (getOption("width", default = NULL))
options(width=2000)
text <- paste(capture.output(print (result_q, width="200")),collapse="\n")
options(width=old.option)
tkconfigure(txt, state="normal")
tryCatch({tkinsert(txt,"end",text)}, error = function(err) {})
tkconfigure(txt, state="disabled")
calculate_q_value_is_running <- FALSE
}
tkconfigure(tbn3,cursor="arrow")
}
shared_mutations <- function(tbn5, txt, smtextEntryA, smtextEntryB, smtextEntryC, cbValue_0sM, cbValue_0sM2, smtextEntryE, smtextEntryF, smtextEntryH, smtextEntryH1, smtextEntryH2, smtextEntryH12, smtextEntryHB, smtextEntryH1B, smtextEntryH2B, smtextEntryH12B, icbValue01, smtextEntryidet){
Require("Biostrings")
Require("parallel")
loaded_files <- .GlobalEnv[["loaded_files"]]
tkconfigure(tbn5,cursor="watch")
if (!calculate_q_value_is_running){
result_q <- c()
if (data.class(result<-try(find.package("SeqFeatR"),TRUE))=="try-error"){
source("assoctuple.R")
}
shared_mutations_is_running <- TRUE
tryCatch({sm_wo_set_input_file_ori_sequences(loaded_files[1,1,8])}, error = function(err) {tkmessageBox(title="An error has occured!",message="No input file",icon="error",type="ok")})
tryCatch({sm_wo_set_input_file_epi_results(loaded_files[1,2,8])}, error = function(err) {tkmessageBox(title="An error has occured!",message="No input file",icon="error",type="ok")})
save_name_sm <- tclvalue(tkgetSaveFile(initialfile="shared_mutations.csv",filetypes="{{csv Files} {.csv}} {{All files} *}"))
if (!nchar(save_name_sm)){
tkmessageBox(message="No file was selected!")
}
tryCatch({result_sm <- assoctuple(loaded_files[1,1,8], loaded_files[1,2,8], as.numeric(tclvalue(smtextEntryA)), as.numeric(tclvalue(smtextEntryB)), as.numeric(tclvalue(smtextEntryC)), save_name_sm, as.numeric(tclvalue(cbValue_0sM)), as.numeric(tclvalue(cbValue_0sM2)), as.numeric(tclvalue(smtextEntryE)), as.numeric(tclvalue(smtextEntryF)), as.numeric(tclvalue(smtextEntryH)), as.numeric(tclvalue(smtextEntryH1)), as.numeric(tclvalue(smtextEntryH2)), as.numeric(tclvalue(smtextEntryH12)), as.numeric(tclvalue(smtextEntryHB)), as.numeric(tclvalue(smtextEntryH1B)), as.numeric(tclvalue(smtextEntryH2B)), as.numeric(tclvalue(smtextEntryH12B)), as.logical(as.numeric(icbValue01)), as.character(tclvalue(smtextEntryidet)) )}, error = function(err) {tkmessageBox(title="An error has occured!",message=paste("No calculation done\n", err),icon="error",type="ok")})
old.option <- (getOption("width", default = NULL))
options(width=2000)
text <- paste(capture.output(print (read.csv2(result_sm), width="200")),collapse="\n")
options(width=old.option)
tkconfigure(txt, state="normal")
tryCatch({tkinsert(txt,"end",text)}, error = function(err) {})
tkconfigure(txt, state="disabled")
shared_mutations_is_running <- FALSE
}
tkconfigure(tbn5,cursor="arrow")
}
rewrite_shared_mutations <- function(tbn3, rsmtextEntryE5, rsmtextEntryE6, rsmtextEntryE7, rsmtextEntryA, rsmtextEntryB, txt){
loaded_files <- .GlobalEnv[["loaded_files"]]
tkconfigure(tbn3,cursor="watch")
if (as.character(tclvalue(rsmtextEntryA)) == "\\t"){
sep <- "\t"
}
else{
sep <- as.character(tclvalue(rsmtextEntryA))
}
if (!rewrite_shared_mutations_is_running){
result_q <- c()
if (data.class(result<-try(find.package("SeqFeatR"),TRUE))=="try-error"){
source("rewritetuple.R")
}
rewrite_shared_mutations_is_running <- TRUE
tryCatch({rsm_wo_set_input_file_epi_results(loaded_files[1,1,10], sep)}, error = function(err) {tkmessageBox(title="An error has occured!",message="No input file",icon="error",type="ok")})
save_name_rsm <- tclvalue(tkgetSaveFile(initialfile="rewritten_shared_mutations.csv",filetypes="{{csv Files} {.csv}} {{All files} *}"))
if (!nchar(save_name_rsm)){
tkmessageBox(message="No file was selected!")
}
tryCatch({result_rsm <- rewrite_shared_mutations_result_inner(loaded_files[1,1,10], save_name_rsm, as.numeric(tclvalue(rsmtextEntryE5)), as.numeric(tclvalue(rsmtextEntryE6)), as.numeric(tclvalue(rsmtextEntryE7)), sep, as.numeric(tclvalue(rsmtextEntryB)))}, error = function(err) {tkmessageBox(title="An error has occured!",message=paste("No calculation done\n", err),icon="error",type="ok")})
old.option <- (getOption("width", default = NULL))
options(width=2000)
text <- paste(capture.output(print(result_rsm)),collapse="\n")
options(width=old.option)
tkconfigure(txt, state="normal")
tryCatch({tkinsert(txt,"end",text)}, error = function(err) {})
tkconfigure(txt, state="disabled")
rewrite_shared_mutations_is_running <- FALSE
}
tkconfigure(tbn3,cursor="arrow")
}
get_freqs <- function(tbn3, gFtextEntryC, gFtextEntryD, gFtextEntryF, gFtextEntryH, gFtextEntryH1, gFtextEntryH2, gFtextEntryH12, gFtextEntryHB, gFtextEntryH1B, gFtextEntryH2B, gFtextEntryH12B, txt){
Require("Biostrings")
Require("ggplot2")
loaded_files <- .GlobalEnv[["loaded_files"]]
tkconfigure(tbn3,cursor="watch")
if (!get_freqs_is_running){
result_q <- c()
if (data.class(result<-try(find.package("SeqFeatR"),TRUE))=="try-error"){
source("getfreqs.R")
}
get_freqs_is_running <- TRUE
tryCatch({gF_wo_set_input_file_known_sequences(loaded_files[1,1,11])}, error = function(err) {tkmessageBox(title="An error has occured!",message=geterrmessage(),icon="error",type="ok")})
tryCatch({gF_wo_set_consensus_file_known_sequences(loaded_files[1,2,11])}, error = function(err) {tkmessageBox(title="An error has occured!",message=geterrmessage(),icon="error",type="ok")})
save_name_gF <- tclvalue(tkgetSaveFile(initialfile="Freqs.csv",filetypes="{{csv Files} {.csv}} {{All files} *}"))
if (!nchar(save_name_gF)){
tkmessageBox(message="No file was selected!")
}
save_name_gFp <- tclvalue(tkgetSaveFile(initialfile="Freqs.png",filetypes="{{png Files} {.png}} {{All files} *}"))
if (!nchar(save_name_gFp)){
tkmessageBox(message="No file was selected!")
}
tryCatch({result_gF <- getfreqs(loaded_files[1,1,11], save_name_gF, save_name_gFp, as.numeric(tclvalue(gFtextEntryC)), as.numeric(tclvalue(gFtextEntryD)), loaded_files[1,2,11], as.numeric(tclvalue(gFtextEntryF)), as.numeric(tclvalue(gFtextEntryH)), as.numeric(tclvalue(gFtextEntryH1)), as.numeric(tclvalue(gFtextEntryH2)), as.numeric(tclvalue(gFtextEntryH12)), as.numeric(tclvalue(gFtextEntryHB)), as.numeric(tclvalue(gFtextEntryH1B)), as.numeric(tclvalue(gFtextEntryH2B)), as.numeric(tclvalue(gFtextEntryH12B)) )}, error = function(err) {tkmessageBox(title="An error has occured!",message=paste("No calculation done\n", err),icon="error",type="ok")})
old.option <- (getOption("width", default = NULL))
options(width=2000)
text <- paste(capture.output(print(result_gF)),collapse="\n")
options(width=old.option)
tkconfigure(txt, state="normal")
tryCatch({tkinsert(txt,"end",text)}, error = function(err) {})
tkconfigure(txt, state="disabled")
get_freqs_is_running <- FALSE
}
tkconfigure(tbn3,cursor="arrow")
}
small_manhattan <- function(tbn3, sMtextEntryC, cbValue_0sM, sMtextEntryF, txt){
Require("ggplot2")
Require("scales")
loaded_files <- .GlobalEnv[["loaded_files"]]
tkconfigure(tbn3,cursor="watch")
if (!small_manhattan_is_running){
result_q <- c()
if (data.class(result<-try(find.package("SeqFeatR"),TRUE))=="try-error"){
source("smallmanhattan.R")
}
small_manhattan_is_running <- TRUE
tryCatch({sM_wo_set_input_file_assoc_result(loaded_files[1,1,12])}, error = function(err) {tkmessageBox(title="An error has occured!",message=geterrmessage(),icon="error",type="ok")})
save_name_sM <- tclvalue(tkgetSaveFile(initialfile="smallManhattan.png",filetypes="{{png Files} {.png}} {{All files} *}"))
if (!nchar(save_name_sM)){
tkmessageBox(message="No file was selected!")
}
save_name_sMs <- tclvalue(tkgetSaveFile(initialfile="smallManhattan.svg",filetypes="{{svg Files} {.svg}} {{All files} *}"))
if (!nchar(save_name_sMs)){
tkmessageBox(message="No file was selected!")
}
tryCatch({result_sM <- smallmanhattan(loaded_files[1,1,12], save_name_sM, save_name_sMs, as.character(tclvalue(sMtextEntryC)), as.logical(as.numeric(cbValue_0sM)), as.character(tclvalue(sMtextEntryF)) )}, error = function(err) {tkmessageBox(title="An error has occured!",message=paste("No calculation done\n", err),icon="error",type="ok")})
old.option <- (getOption("width", default = NULL))
options(width=2000)
text <- paste(capture.output(print(result_sM)),collapse="\n")
options(width=old.option)
tkconfigure(txt, state="normal")
tryCatch({tkinsert(txt,"end",text)}, error = function(err) {})
tkconfigure(txt, state="disabled")
small_manhattan_is_running <- FALSE
}
tkconfigure(tbn3,cursor="arrow")
}
#----------------------------------------------------------
SeqFeatR_GUI <- structure(function(
### SeqFeatR GUI to handle the program without command line
){
loaded_files <- array(rep(0, 48), dim=c(1,4,12), dimnames = list("name",c("specific file_1","specific file_2","specific file_3", "specific file_4"),c("pos_epi", "co-mut", "q-value", "pos_e_cal", "graphics_co_mut", "founder_elim", "two_side", "shared_mutations", "co_mut_graphics_both", "rewrite_shared_mutations", "get_freqs", "small_manhattan")))
.GlobalEnv[["loaded_files"]] <- loaded_files
if(length(system.file("extdata", "config.cfg", package="SeqFeatR")) > 1){
con <- read.config(system.file("extdata", "config.cfg", package="SeqFeatR"))
}else {
con <- c()
}
tt <- tktoplevel()
topMenu <- tkmenu(tt) # Create a menu
tkconfigure(tt, menu = topMenu)
fileMenu <- tkmenu(topMenu, tearoff = FALSE)
helpMenu <- tkmenu(topMenu, tearoff = FALSE)
openRecentMenu <- tkmenu(topMenu, tearoff = FALSE)
tkadd(fileMenu, "command", label = "Open config file", command = function() attach.config(tclvalue(tkgetOpenFile(initialfile = "config.cfg", filetypes = "{{Config Files} {.cfg}} {{All files} *}"))))
tkadd(fileMenu, "command", label = "Save config file", command = function() save_config(z))
tkadd(fileMenu, "command", label = "Generate example fasta", command = function() generate_example_fasta())
tkadd(fileMenu, "command", label = "Generate example config", command = function() generate_example_config())
tkadd(fileMenu, "command", label = "Generate example config without HLA", command = function() generate_example_config_wo_HLA())
tkadd(fileMenu, "command", label = "Quit", command = function() tkdestroy(tt))
tkadd(helpMenu, "command", label = "Tutorial", command = function() open_tutorial())
tkadd(helpMenu, "command", label = "About SeqFeatR", command = function() about())
tkadd(topMenu, "cascade", label = "File", menu = fileMenu)
tkadd(topMenu, "cascade", label = "Help", menu = helpMenu)
frameOverall <- tkframe(tt)
frame_progs <- tkframe(frameOverall,relief="groove",borderwidth=2, background="white")
frame_info <- tkframe(frameOverall,relief="groove",borderwidth=2)
frame_bar <- tkframe(frameOverall,relief="sunken",borderwidth=2)
tkpack(frameOverall, fill="both",expand="yes")
tkgrid(frame_progs, sticky="snew")
tkgrid(frame_info)
tkgrid(frame_bar, sticky="snew")
#------------------------------------------------------------------------------------------------------------------------------
#tn <- tkwidget(frame_progs, "ttk::notebook")
#print (.Tcl.args(background="red"))
tcl("ttk::style", "configure", "TNotebook", background="white")
# Make non selected tabs a little darker
tcl("ttk::style", "configure", "TNotebook.Tab", background="lightgrey")
#tcl("ttk::style", "map", "TNotebook.Tab", background=c("active", "skyblue"))
#tcl("ttk::style", "map", "TNotebook.Tab", background=c("active", "red"))
tcl("ttk::style", "map", "TNotebook.Tab", background=c("selected","khaki1"))
tn <- ttknotebook(frame_progs)
#tkwm.resizable(tt, TRUE, TRUE)### FOR WINDOWS COMMENT OUT!!
tkwm.title(tt, "SeqFeatR for the discovery of feature-sequence associations")
tkgrid.columnconfigure(tt,0,weight=1)
tkgrid.rowconfigure(tt,0,weight=1)
tkwm.minsize(tt, "1024", "680")
tkgrid.rowconfigure(frameOverall,1,weight=1, minsize=100)
tkgrid.rowconfigure(frameOverall,0,weight=10, minsize=200)
tkgrid.columnconfigure(frameOverall,0,weight=1, minsize=100)
#tkgrid.configure(frameOverall,sticky='nswe')
tkgrid.rowconfigure(frame_progs,0,weight=1, minsize=20)
tkgrid.rowconfigure(frame_progs,1,weight=100, minsize=100)
tkgrid.columnconfigure(frame_progs,0,weight=1, minsize=10)
tkgrid.configure(frame_progs,sticky='nswe')
tkgrid.rowconfigure(frame_info,1,weight=1, minsize=10)
tkgrid.columnconfigure(frame_info,1,weight=1, minsize=10)
tkgrid.rowconfigure(frame_bar,1,weight=1, minsize=10)
tkgrid.columnconfigure(frame_bar,1,weight=1, minsize=10)
#-----------------------------------------------------------------------------------------------------------------------------
info <- tclVar("*: Please fill in before you hit the corresponding start button. You can generate and load an example configuration under the 'File' menu.")
l <- tklabel(frame_bar, textvariable=info)
tkgrid(l, sticky="snew")
#-----------------------------------------------------------------------------------------------------------------------------
dna <- tkframe(frame_progs)
tkgrid(dna)
tkgrid.rowconfigure(dna,0,weight=0)
tkgrid.columnconfigure(dna,0,weight=0)
cb01 <- tkcheckbutton(dna,command=function()check_dna(cbValu01 <- as.character(tclvalue(cbValue01))), background="#FF6600")
cbValue01 <- tclVar("0")
tkconfigure(cb01,variable=cbValue01)
icb01 <- tkcheckbutton(dna,command=function()check_ident(icbValu01 <- as.character(tclvalue(icbValue01)), textEntryWidgetH, textEntryWidgetH1, textEntryWidgetH12, textEntryWidgetH2, textEntryWidgetHB, textEntryWidgetH1B, textEntryWidgetH12B, textEntryWidgetH2B, textEntryWidgetHC, textEntryWidgetH1C, textEntryWidgetH2C, textEntryWidgetH12C, textEntryWidgetHBC, textEntryWidgetH1BC, textEntryWidgetH2BC, textEntryWidgetH12BC, smtextEntryWidgetX, smtextEntryWidgetH, smtextEntryWidgetH1, smtextEntryWidgetH2, smtextEntryWidgetH12, smtextEntryWidgetHB, smtextEntryWidgetH1B, smtextEntryWidgetH2B, smtextEntryWidgetH12B), background="#FF6600")
icbValue01 <- tclVar("0")
tkconfigure(icb01,variable=icbValue01)
tkgrid(tklabel(dna,text="Fasta files with nucleotides?", background="#FF6600"), cb01, tklabel(dna,text="One feature?", background="#FF6600"), icb01 )
#-----------------------------------------------------------------------------------------------------------------------------
tkgrid.rowconfigure(tn,0,weight=5)
tkgrid.columnconfigure(tn,0,weight=5)
tkgrid.configure(tn,sticky='nswe')
otbn <- ttkframe(tn)
otbn2 <- ttkframe(tn)
otbn3 <- ttkframe(tn)
otbn5 <- ttkframe(tn)
tkadd(tn,otbn,text="Point mutations vs. feature(s)") ### tabid=0
tkadd(tn,otbn2,text="n-Tuple vs. feature(s)") ### tabid=1
tkadd(tn,otbn5,text="Graphics for n-tuple calculations") ### tabid=5
tkadd(tn,otbn3,text="Add-on scripts") ### tabid=3
#------------------------------------------------------------------------------------------------------------------------------
scr <- tkscrollbar(frame_info, repeatinterval=5, command=function(...)tkyview(txt,...))
xscr <- tkscrollbar(frame_info, repeatinterval=5, command=function(...)tkxview(txt,...),orient='horiz')
txt <- tktext(frame_info,bg="white", font="Helvetica", height=15, width=80, wrap="none", yscrollcommand=function(...)tkset(scr,...), xscrollcommand=function(...)tkset(xscr,...))
tkgrid(txt,scr)
tkgrid(xscr)
tkgrid.configure(scr,sticky="ns")
tkgrid.configure(xscr,sticky="ew")
tkconfigure(txt, state="disabled")
tkgrid.rowconfigure(txt,0,weight=1)
tkgrid.columnconfigure(txt,0,weight=1)
tkgrid.configure(txt,sticky='nswe')
#---------------------------------------------------
tkgrid.rowconfigure(otbn,0,weight=1, minsize=100)
tkgrid.columnconfigure(otbn,0,weight=10, minsize=200)
tkgrid.columnconfigure(otbn,1,weight=3, minsize=100)
tbn <- ttkframe(otbn)
helptbn <- ttkframe(otbn)
tkgrid(tbn, helptbn, sticky="snew")
tkgrid.columnconfigure(tbn,0,weight=9)
tkgrid.columnconfigure(helptbn,0,weight=1)
scr1 <- tkscrollbar(tbn, command=function(...)tkyview(txt1,...),bg='white')
txt1 <- tktext(tbn,height=1, width=33, bg='grey')
xscr1 <- tkscrollbar(tbn, command=function(...)tkxview(txt1,...),orient='horiz')
tkconfigure(txt1, yscrollcommand=function(...)tkset(scr1,...), xscrollcommand=function(...)tkset(xscr1,...), state="disabled")
tkpack(scr1,side='right',fill='y')
tkpack(txt1,expand='yes',fill='both')
tkpack(xscr1, side="bottom", fill="x")
sf1 <- tkcanvas(txt1, background="white")
tkwindow.create(txt1, 'end', window=sf1)
epi <- tkframe(sf1,relief="groove",borderwidth=2)
epist <- tkframe(sf1,relief="groove",borderwidth=2)
tkgrid(epi, sticky="e")
tkgrid(epist, sticky="snew")
lb1 <- tklabel(epi, text=paste("Discover associations between point mutations and feature(s)"), background="#FFCC99")
tkgrid (lb1, sticky="snew", columnspan=9)
button.widget_epi1 <- tkbutton(epi,text="Select FASTA file",command=function()getFASTAfile(pElabelText1, 1, 1))
pElabelText <- tclVar("Sequence alignment to analyse *: ")
pElabel1 <- tklabel(epi,text=tclvalue(pElabelText))
tkconfigure(pElabel1,textvariable=pElabelText)
pElabelText1 <- tclVar("")
pElabel2 <- tklabel(epi,text=tclvalue(pElabelText1))
tkconfigure(pElabel2,textvariable=pElabelText1)
tkgrid(pElabel1, pElabel2, button.widget_epi1)
button.widget_epi2 <- tkbutton(epi,text="Select csv file",command=function()getcsvfile(pElabelText1A, 1, 2))
pElabelTextA <- tclVar("Known epitopes: ")
pElabel1A <- tklabel(epi,text=tclvalue(pElabelTextA))
tkconfigure(pElabel1A,textvariable=pElabelTextA)
pElabelText1A <- tclVar("")
pElabel2A <- tklabel(epi,text=tclvalue(pElabelText1A))
tkconfigure(pElabel2A,textvariable=pElabelText1A)
tkgrid(pElabel1A, pElabel2A, button.widget_epi2)
button.widget_epi3 <- tkbutton(epi,text="Select csv file",command=function()getcsvfile(pElabelText1B, 1, 3))
pElabelTextB <- tclVar("Known binding motifs: ")
pElabel1B <- tklabel(epi,text=tclvalue(pElabelTextB))
tkconfigure(pElabel1B,textvariable=pElabelTextB)
button.widget_epi4 <- tkbutton(epi,text="Select FASTA File",command=function()getFASTAfile(pElabelText1D, 1, 4))
pElabelTextD <- tclVar("Reference sequence: ")
pElabel1D <- tklabel(epi,text=tclvalue(pElabelTextD))
tkconfigure(pElabel1D,textvariable=pElabelTextD)
pElabelText1D <- tclVar("")
pElabel2D <- tklabel(epi,text=tclvalue(pElabelText1D))
tkconfigure(pElabel2D,textvariable=pElabelText1D)
tkgrid(pElabel1D, pElabel2D, button.widget_epi4)
pElabelText1B <- tclVar("")
pElabel2B <- tklabel(epi,text=tclvalue(pElabelText1B))
tkconfigure(pElabel2B,textvariable=pElabelText1B)
tkgrid(pElabel1B, pElabel2B, button.widget_epi3)
pElabelTextH <- tclVar("Position of feature A *: ")
pElabel1H <- tklabel(epi,text=tclvalue(pElabelTextH))
if (length(con[which(con[,1]=="HLA-A1"),2]) > 0){
textEntryH <- tclVar(con[which(con[,1]=="HLA-A1"),2])
}else{
textEntryH <- tclVar("")
}
textEntryWidgetH <- tkentry(epi,width=3,textvariable=textEntryH)
pElabelTextH1 <- tclVar("-")
pElabel1H1 <- tklabel(epi,text=tclvalue(pElabelTextH1))
if (length(con[which(con[,1]=="HLA-A2"),2]) > 0){
textEntryH1 <- tclVar(con[which(con[,1]=="HLA-A2"),2])
}else{
textEntryH1 <- tclVar("")
}
textEntryWidgetH1 <- tkentry(epi,width=3,textvariable=textEntryH1)
if (length(con[which(con[,1]=="HLA-A3"),2]) > 0){
textEntryH2 <- tclVar(con[which(con[,1]=="HLA-A3"),2])
}else{
textEntryH2 <- tclVar("")
}
textEntryWidgetH2 <- tkentry(epi,width=3,textvariable=textEntryH2)
pElabelTextH12 <- tclVar("-")
pElabel1H12 <- tklabel(epi,text=tclvalue(pElabelTextH12))
if (length(con[which(con[,1]=="HLA-A4"),2]) > 0){
textEntryH12 <- tclVar(con[which(con[,1]=="HLA-A4"),2])
}else{
textEntryH12 <- tclVar("")
}
textEntryWidgetH12 <- tkentry(epi,width=3,textvariable=textEntryH12)
tkgrid(pElabel1H, textEntryWidgetH, pElabel1H1, textEntryWidgetH1, textEntryWidgetH2, pElabel1H12, textEntryWidgetH12)
pElabelTextHB <- tclVar("Position of feature B *: ")
pElabel1HB <- tklabel(epi,text=tclvalue(pElabelTextHB))
if (length(con[which(con[,1]=="HLA-B1"),2]) > 0){
textEntryHB <- tclVar(con[which(con[,1]=="HLA-B1"),2])
}else{
textEntryHB <- tclVar("")
}
textEntryWidgetHB <- tkentry(epi,width=3,textvariable=textEntryHB)
pElabelTextH1B <- tclVar("-")
pElabel1H1B <- tklabel(epi,text=tclvalue(pElabelTextH1B))
if (length(con[which(con[,1]=="HLA-B2"),2]) > 0){
textEntryH1B <- tclVar(con[which(con[,1]=="HLA-B2"),2])
}else{
textEntryH1B <- tclVar("")
}
textEntryWidgetH1B <- tkentry(epi,width=3,textvariable=textEntryH1B)
if (length(con[which(con[,1]=="HLA-B3"),2]) > 0){
textEntryH2B <- tclVar(con[which(con[,1]=="HLA-B3"),2])
}else{
textEntryH2B <- tclVar("")
}
textEntryWidgetH2B <- tkentry(epi,width=3,textvariable=textEntryH2B)
pElabelTextH12B <- tclVar("-")
pElabel1H12B <- tklabel(epi,text=tclvalue(pElabelTextH12B))
if (length(con[which(con[,1]=="HLA-B4"),2]) > 0){
textEntryH12B <- tclVar(con[which(con[,1]=="HLA-B4"),2])
}else{
textEntryH12B <- tclVar("")
}
textEntryWidgetH12B <- tkentry(epi,width=3,textvariable=textEntryH12B)
tkgrid(pElabel1HB, textEntryWidgetHB, pElabel1H1B, textEntryWidgetH1B, textEntryWidgetH2B, pElabel1H12B, textEntryWidgetH12B)
cb0eG1C <- tkcheckbutton(epi,command=function()has_C_allel(cbValue_0eG1C <- as.character(tclvalue(cbValue_0eG1C)), textEntryWidgetHCC, textEntryWidgetH1CC, textEntryWidgetH2CC, textEntryWidgetH12CC))
if (length(con[which(con[,1]=="C_allel"),2]) > 0){
cbValue_0eG1C <- tclVar(con[which(con[,1]=="has_C"),2])
}else{
cbValue_0eG1C <- tclVar("0")
}
tkconfigure(cb0eG1C,variable=cbValue_0eG1C)
tkgrid(tklabel(epi,text="FASTA header has C allel information?"),cb0eG1C, sticky="snew")
pElabelTextHCC <- tclVar("Position of feature C *: ")
pElabel1HCC <- tklabel(epi,text=tclvalue(pElabelTextHCC))
if (length(con[which(con[,1]=="HLA-C1"),2]) > 0){
textEntryHCC <- tclVar(con[which(con[,1]=="HLA-C1"),2])
}else{
textEntryHCC <- tclVar("")
}
textEntryWidgetHCC <- tkentry(epi,width=3,textvariable=textEntryHCC)
pElabelTextH1CC <- tclVar("-")
pElabel1H1CC <- tklabel(epi,text=tclvalue(pElabelTextH1CC))
if (length(con[which(con[,1]=="HLA-C2"),2]) > 0){
textEntryH1CC <- tclVar(con[which(con[,1]=="HLA-C2"),2])
}else{
textEntryH1CC <- tclVar("")
}
textEntryWidgetH1CC <- tkentry(epi,width=3,textvariable=textEntryH1CC)
if (length(con[which(con[,1]=="HLA-C3"),2]) > 0){
textEntryH2CC <- tclVar(con[which(con[,1]=="HLA-C3"),2])
}else{
textEntryH2CC <- tclVar("")
}
textEntryWidgetH2CC <- tkentry(epi,width=3,textvariable=textEntryH2CC)
pElabelTextH12CC <- tclVar("-")
pElabel1H12CC <- tklabel(epi,text=tclvalue(pElabelTextH12CC))
if (length(con[which(con[,1]=="HLA-C4"),2]) > 0){
textEntryH12CC <- tclVar(con[which(con[,1]=="HLA-C4"),2])
}else{
textEntryH12CC <- tclVar("")
}
textEntryWidgetH12CC <- tkentry(epi,width=3,textvariable=textEntryH12CC)
tkgrid(pElabel1HCC, textEntryWidgetHCC, pElabel1H1CC, textEntryWidgetH1CC, textEntryWidgetH2CC, pElabel1H12CC, textEntryWidgetH12CC)
tkconfigure(textEntryWidgetHCC, state="disabled")
tkconfigure(textEntryWidgetH1CC, state="disabled")
tkconfigure(textEntryWidgetH2CC, state="disabled")
tkconfigure(textEntryWidgetH12CC, state="disabled")
pElabelTextC <- tclVar("Minimal number of members *: ")
pElabel1C <- tklabel(epi,text=tclvalue(pElabelTextC))
if (length(con[which(con[,1]=="Number of patients threshold"),2]) > 0){
textEntryC <- tclVar(con[which(con[,1]=="Number of patients threshold"),2])
}else{
textEntryC <- tclVar("")
}
textEntryWidgetC <- tkentry(epi,textvariable=textEntryC)
tkgrid(pElabel1C, textEntryWidgetC)
pElabelTextD <- tclVar("Height of horizontal line *: ")
pElabel1D2 <- tklabel(epi,text=tclvalue(pElabelTextD))
if (length(con[which(con[,1]=="Height of horizontal bar"),2]) > 0){
textEntryD <- tclVar(con[which(con[,1]=="Height of horizontal bar"),2])
}else{
textEntryD <- tclVar("")
}
textEntryWidgetD <- tkentry(epi,textvariable=textEntryD)
tkgrid(pElabel1D2, textEntryWidgetD)
pElabelTextE <- tclVar("Height of star level *: ")
pElabel1E <- tklabel(epi,text=tclvalue(pElabelTextE))
if (length(con[which(con[,1]=="Height of star level"),2]) > 0){
textEntryE <- tclVar(con[which(con[,1]=="Height of star level"),2])
}else{
textEntryE <- tclVar("")
}
textEntryWidgetE <- tkentry(epi,textvariable=textEntryE)
tkgrid(pElabel1E, textEntryWidgetE)
cb0eG1 <- tkcheckbutton(epi)
if (length(con[which(con[,1]=="pos_epi_plot"),2]) > 0){
cbValue_0eG1 <- tclVar(con[which(con[,1]=="pos_epi_plot"),2])
}else{
cbValue_0eG1 <- tclVar("0")
}
tkconfigure(cb0eG1,variable=cbValue_0eG1)
tkgrid(tklabel(epi,text="Show 'possible epitopes plot' (pdf)?"),cb0eG1, sticky="snew")
pElabelTextH42B <- tclVar("Window size: ")
pElabelH42B <- tklabel(epi,text=tclvalue(pElabelTextH42B))
if (length(con[which(con[,1]=="window_size"),2]) > 0){
textEntryH42B <- tclVar(con[which(con[,1]=="window_size"),2])
}else{
textEntryH42B <- tclVar("")
}
textEntryWidgetH42B <- tkentry(epi,textvariable=textEntryH42B)
tkgrid(pElabelH42B, textEntryWidgetH42B)
pElabelTextIB <- tclVar("P-value correction *: ")
pElabel1IB <- tklabel(epi,text=tclvalue(pElabelTextIB))
ddb <- tkframe(epi)
textEntryIB <- tclVar()
dropdownList(ddb, c("holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none"), textEntryIB, 15, "none")
tkgrid(pElabel1IB, ddb)
cb0e <- tkcheckbutton(epi)#,command=function()check_phylo(cbValu_0e <- as.character(tclvalue(cbValue_0e)), textEntryWidgetKIB))
if (length(con[which(con[,1]=="Phylogenetic comparison"),2]) > 0){
cbValue_0e <- tclVar(con[which(con[,1]=="Phylogenetic comparison"),2])
}else{
cbValue_0e <- tclVar("0")
}
tkconfigure(cb0e,variable=cbValue_0e)
tkgrid(tklabel(epi,text="Check for phylogenetic bias?"),cb0e, sticky="snew")
cbbayes_factor <- tkcheckbutton(epi,command=function()check_bayes_factor(cbValue_bayes_factor <- as.character(tclvalue(cbValue_bayes_factor)), cbValue_K <- as.character(tclvalue(cbValue_K)), textEntryWidgetdirichlet_precision_parameter))
if (length(con[which(con[,1]=="Bayes factor"),2]) > 0){
cbValue_bayes_factor <- tclVar(con[which(con[,1]=="Bayes factor"),2])
}else{
cbValue_bayes_factor <- tclVar("0")
}
tkconfigure(cbbayes_factor,variable=cbValue_bayes_factor)
tkgrid(tklabel(epi,text="Calculation with Bayes Factor?", foreground="goldenrod"),cbbayes_factor, sticky="snew")
cbconK_factor <- tkcheckbutton(epi,command=function()check_K(cbValue_bayes_factor <- as.character(tclvalue(cbValue_bayes_factor)), cbValue_K <- as.character(tclvalue(cbValue_K)), textEntryWidgetdirichlet_precision_parameter))
if (length(con[which(con[,1]=="Bayes factor"),2]) > 0){
cbValue_K <- tclVar(con[which(con[,1]=="constant K"),2])
}else{
cbValue_K <- tclVar("0")
}
tkconfigure(cbconK_factor,variable=cbValue_K)
tkgrid(tklabel(epi,text="Calculation with constant\n Dirichlet precision parameter?", foreground="goldenrod"),cbconK_factor, sticky="snew")
pElabelTextdirichlet_precision_parameter <- tclVar("Dirichlet precision parameter: ")
pElabel1dirichlet_precision_parameter <- tklabel(epi,text=tclvalue(pElabelTextdirichlet_precision_parameter))
if (length(con[which(con[,1]=="Dirichlet precision parameter"),2]) > 0){
dirichlet_precision_parameter_textEntry <- tclVar(con[which(con[,1]=="Dirichlet precision parameter"),2])
}else{
dirichlet_precision_parameter_textEntry <- tclVar("")
}
textEntryWidgetdirichlet_precision_parameter <- tkentry(epi,textvariable=dirichlet_precision_parameter_textEntry)
tkconfigure(textEntryWidgetdirichlet_precision_parameter, state="disabled")
tkgrid(pElabel1dirichlet_precision_parameter, textEntryWidgetdirichlet_precision_parameter)
###set left:
tkgrid.configure(pElabel1,sticky="w")
tkgrid.configure(pElabel1A,sticky="w")
tkgrid.configure(pElabel1B,sticky="w")
tkgrid.configure(pElabel1D,sticky="w")
tkgrid.configure(pElabel1C,sticky="w")
tkgrid.configure(pElabel1D2,sticky="w")
tkgrid.configure(pElabel1E,sticky="w")
tkgrid.configure(pElabel1H,sticky="w")
tkgrid.configure(pElabel1HB,sticky="w")
tkgrid.configure(pElabel1HCC,sticky="w")
tkgrid.configure(pElabel1IB,sticky="w")
tkgrid.configure(pElabelH42B,sticky="w")
tkgrid.configure(pElabel1dirichlet_precision_parameter,sticky="w")
OK.bute1 <- tkbutton(epi,text="Start", foreground = "red",command=function()calculate_pos_epi(tbn, cbValue01, cbValue_0e, textEntryC, textEntryD, textEntryE, textEntryH, textEntryH1, textEntryH2, textEntryH12, textEntryHB, textEntryH1B, textEntryH2B, textEntryH12B, textEntryHCC, textEntryH1CC, textEntryH2CC, textEntryH12CC, as.character(tclvalue(cbValue_0eG1C)), textEntryIB, txt, as.character(tclvalue(icbValue01)), textEntryH42B, cbValue_0eG1, as.character(tclvalue(cbValue_bayes_factor)), as.character(tclvalue(cbValue_K)), dirichlet_precision_parameter_textEntry ))
tkgrid(OK.bute1)
tkgrid.configure(button.widget_epi1, column=8, sticky="e")
tkgrid.configure(button.widget_epi2, column=8, sticky="e")
tkgrid.configure(button.widget_epi3, column=8, sticky="e")
tkgrid.configure(button.widget_epi4, column=8, sticky="e")
tkgrid.configure(OK.bute1, column=8, sticky="e")
tkgrid.configure(pElabel2, column=2, columnspan=6, sticky="w")
tkgrid.configure(pElabel2A, column=2, columnspan=6, sticky="w")
tkgrid.configure(pElabel2B, column=2, columnspan=6, sticky="w")
tkgrid.configure(pElabel2D, column=2, columnspan=6, sticky="w")
tkgrid.configure(textEntryWidgetC, column=2, columnspan=6)
tkgrid.configure(textEntryWidgetD, column=2, columnspan=6)
tkgrid.configure(textEntryWidgetE, column=2, columnspan=6)
tkgrid.configure(ddb, column=2, columnspan=6)
tkgrid.configure(textEntryWidgetH42B, column=2, columnspan=6)
tkgrid.configure(cb0eG1, column=2, columnspan=6)
tkgrid.configure(cb0eG1C, column=2, columnspan=6)
tkgrid.configure(cb0e, column=2, columnspan=6)
tkgrid.configure(cbbayes_factor, column=2, columnspan=6)
tkgrid.configure(cbconK_factor, column=2, columnspan=6)
tkgrid.configure(textEntryWidgetdirichlet_precision_parameter, column=2, columnspan=6)
tkgrid.configure(textEntryWidgetH, column=2)
tkgrid.configure(pElabel1H1, column=3)
tkgrid.configure(textEntryWidgetH1, column=4)
tkgrid.configure(textEntryWidgetH2, column=5)
tkgrid.configure(pElabel1H12, column=6)
tkgrid.configure(textEntryWidgetH12, column=7)
tkgrid.configure(textEntryWidgetHB, column=2)
tkgrid.configure(pElabel1H1B, column=3)
tkgrid.configure(textEntryWidgetH1B, column=4)
tkgrid.configure(textEntryWidgetH2B, column=5)
tkgrid.configure(pElabel1H12B, column=6)
tkgrid.configure(textEntryWidgetH12B, column=7)
tkgrid.configure(textEntryWidgetHCC, column=2)
tkgrid.configure(pElabel1H1CC, column=3)
tkgrid.configure(textEntryWidgetH1CC, column=4)
tkgrid.configure(textEntryWidgetH2CC, column=5)
tkgrid.configure(pElabel1H12CC, column=6)
tkgrid.configure(textEntryWidgetH12CC, column=7)
#-----------------------------------------------------------
lb1 <- tklabel(epist, text=paste("Visualize odds ratios and p-values"), background="#FFCC99")
tkgrid (lb1, sticky="snew", columnspan=8)
Bbutton.widget_epi <- tkbutton(epist,text="Select csv file",command=function()getcsvfile(BpElabelText1, 7, 1))
BpElabelText <- tclVar("Result file from point mutations *: ")
BpElabel1 <- tklabel(epist,text=tclvalue(BpElabelText))
tkconfigure(BpElabel1,textvariable=BpElabelText)
BpElabelText1 <- tclVar("")
BpElabel2 <- tklabel(epist,text=tclvalue(BpElabelText1))
tkconfigure(BpElabel2,textvariable=BpElabelText1)
tkgrid(BpElabel1, BpElabel2, Bbutton.widget_epi)
BpElabelTextA <- tclVar("csv seperator *: ")
BpElabel1A <- tklabel(epist,text=tclvalue(BpElabelTextA))
if (length(con[which(con[,1]=="csv seperator"),2]) > 0){
BtextEntryA <- tclVar(con[which(con[,1]=="csv seperator"),2])
}else{
BtextEntryA <- tclVar("")
}
BtextEntryWidgetA <- tkentry(epist,textvariable=BtextEntryA)
tkgrid(BpElabel1A, BtextEntryWidgetA)
BpElabelTextB <- tclVar("# different features in input file *: ")
BpElabel1B <- tklabel(epist,text=tclvalue(BpElabelTextB))
if (length(con[which(con[,1]=="number of cases"),2]) > 0){
BtextEntryB <- tclVar(con[which(con[,1]=="number of cases"),2])
}else{
BtextEntryB <- tclVar("")
}
BtextEntryWidgetB <- tkentry(epist,textvariable=BtextEntryB)
tkgrid(BpElabel1B, BtextEntryWidgetB)
BpElabelTextC <- tclVar("First column nr. of odds-ratio *: ")
BpElabel1C <- tklabel(epist,text=tclvalue(BpElabelTextC))
if (length(con[which(con[,1]=="position of odds.ratio"),2]) > 0){
BtextEntryC <- tclVar(con[which(con[,1]=="position of odds.ratio"),2])
}else{
BtextEntryC <- tclVar("")
}
BtextEntryWidgetC <- tkentry(epist,textvariable=BtextEntryC)
tkgrid(BpElabel1C, BtextEntryWidgetC)
BpElabelTextD <- tclVar("First column nr. of p-values *: ")
BpElabel1D <- tklabel(epist,text=tclvalue(BpElabelTextD))
if (length(con[which(con[,1]=="position of p.values"),2]) > 0){
BtextEntryD <- tclVar(con[which(con[,1]=="position of p.values"),2])
}else{
BtextEntryD <- tclVar("")
}
BtextEntryWidgetD <- tkentry(epist,textvariable=BtextEntryD)
tkgrid(BpElabel1D, BtextEntryWidgetD)
BpElabelTextE <- tclVar("Column nr. for name (y-axis label) *: ")
BpElabel1E <- tklabel(epist,text=tclvalue(BpElabelTextE))
if (length(con[which(con[,1]=="name for the y-axis label"),2]) > 0){
BtextEntryE <- tclVar(con[which(con[,1]=="name for the y-axis label"),2])
}else{
BtextEntryE <- tclVar("")
}
BtextEntryWidgetE <- tkentry(epist,textvariable=BtextEntryE)
tkgrid(BpElabel1E, BtextEntryWidgetE)
BpElabelTextF <- tclVar("Nr. of columns for one feature *: ")
BpElabel1F <- tklabel(epist,text=tclvalue(BpElabelTextF))
if (length(con[which(con[,1]=="frequency"),2]) > 0){
BtextEntryF <- tclVar(con[which(con[,1]=="frequency"),2])
}else{
BtextEntryF <- tclVar("")
}
BtextEntryWidgetF <- tkentry(epist,textvariable=BtextEntryF)
tkgrid(BpElabel1F, BtextEntryWidgetF)
BpElabelTextG <- tclVar("First column nr. of sequence letter: ")
BpElabel1G <- tklabel(epist,text=tclvalue(BpElabelTextG))
if (length(con[which(con[,1]=="position of amino acid"),2]) > 0){
BtextEntryG <- tclVar(con[which(con[,1]=="position of amino acid"),2])
}else{
BtextEntryG <- tclVar("")
}
BtextEntryWidgetG <- tkentry(epist,textvariable=BtextEntryG)
tkgrid(BpElabel1G, BtextEntryWidgetG)
BpElabelTextH <- tclVar("Maximum value on y-axis *: ")
BpElabel1H <- tklabel(epist,text=tclvalue(BpElabelTextH))
if (length(con[which(con[,1]=="maximum value of y-axis"),2]) > 0){
BtextEntryH <- tclVar(con[which(con[,1]=="maximum value of y-axis"),2])
}else{
BtextEntryH <- tclVar("")
}
BtextEntryWidgetH <- tkentry(epist,textvariable=BtextEntryH)
tkgrid(BpElabel1H, BtextEntryWidgetH)
BpElabelTextI <- tclVar("Ticks on y-axis *: ")
BpElabel1I <- tklabel(epist,text=tclvalue(BpElabelTextI))
if (length(con[which(con[,1]=="intervall of y-axis"),2]) > 0){
BtextEntryI <- tclVar(con[which(con[,1]=="intervall of y-axis"),2])
}else{
BtextEntryI <- tclVar("")
}
BtextEntryWidgetI <- tkentry(epist,textvariable=BtextEntryI)
tkgrid(BpElabel1I, BtextEntryWidgetI)
BpElabelTextJ <- tclVar("First column for add. color information: ")
BpElabel1J <- tklabel(epist,text=tclvalue(BpElabelTextJ))
if (length(con[which(con[,1]=="add color information"),2]) > 0){
BtextEntryJ <- tclVar(con[which(con[,1]=="add color information"),2])
}else{
BtextEntryJ <- tclVar("")
}
BtextEntryWidgetJ <- tkentry(epist,textvariable=BtextEntryJ)
tkgrid(BpElabel1J, BtextEntryWidgetJ)
BpElabelTextK <- tclVar("Bias in color *: ")
BpElabel1K <- tklabel(epist,text=tclvalue(BpElabelTextK))
if (length(con[which(con[,1]=="bias"),2]) > 0){
BtextEntryK <- tclVar(con[which(con[,1]=="bias"),2])
}else{
BtextEntryK <- tclVar("")
}
BtextEntryWidgetK <- tkentry(epist,textvariable=BtextEntryK)
tkgrid(BpElabel1K, BtextEntryWidgetK)
BpElabelTextL <- tclVar("Height equals p-values or odds ratios *: ")
BpElabel1L <- tklabel(epist,text=tclvalue(BpElabelTextL))
ddb2 <- tkframe(epist)
BtextEntryL <- tclVar()
dropdownList(ddb2, c("P", "OR"), BtextEntryL, 15, "P")
tkgrid(BpElabel1L, ddb2)
BOK.bute2 <- tkbutton(epist,text="Start", foreground = "red",command=function()create_sequence_graphic_G(tbn, BtextEntryA, BtextEntryB, BtextEntryC, BtextEntryD, BtextEntryE, BtextEntryF, BtextEntryG, BtextEntryH, BtextEntryI, txt, BtextEntryJ, BtextEntryK, BtextEntryL))
tkgrid(BOK.bute2)
###set left:
tkgrid.configure(BpElabel1, sticky="w")
tkgrid.configure(BpElabel1A, sticky="w")
tkgrid.configure(BpElabel1B, sticky="w")
tkgrid.configure(BpElabel1C, sticky="w")
tkgrid.configure(BpElabel1D, sticky="w")
tkgrid.configure(BpElabel1E, sticky="w")
tkgrid.configure(BpElabel1F, sticky="w")
tkgrid.configure(BpElabel1G, sticky="w")
tkgrid.configure(BpElabel1H, sticky="w")
tkgrid.configure(BpElabel1I, sticky="w")
tkgrid.configure(BpElabel1J, sticky="w")
tkgrid.configure(BpElabel1K, sticky="w")
tkgrid.configure(BpElabel1L, sticky="w")
tkgrid.configure(Bbutton.widget_epi, column=3, sticky="e")
tkgrid.configure(BOK.bute2, column=3, sticky="e")
tkgrid.configure(BpElabel2, column=2)
tkgrid.configure(BtextEntryWidgetA, column=2)
tkgrid.configure(BtextEntryWidgetB, column=2)
tkgrid.configure(BtextEntryWidgetC, column=2)
tkgrid.configure(BtextEntryWidgetD, column=2)
tkgrid.configure(BtextEntryWidgetE, column=2)
tkgrid.configure(BtextEntryWidgetF, column=2)
tkgrid.configure(BtextEntryWidgetG, column=2)
tkgrid.configure(BtextEntryWidgetH, column=2)
tkgrid.configure(BtextEntryWidgetI, column=2)
tkgrid.configure(BtextEntryWidgetJ, column=2)
tkgrid.configure(BtextEntryWidgetK, column=2)
tkgrid.configure(ddb2, column=2)
#--------------------------------------------------------------------------------------------------------------------------------
tkgrid.rowconfigure(otbn2,0,weight=1, minsize=100)
tkgrid.columnconfigure(otbn2,0,weight=10, minsize=200)
tkgrid.columnconfigure(otbn2,1,weight=3, minsize=100)
tbn2 <- ttkframe(otbn2)
helptbn2 <- ttkframe(otbn2)
tkgrid(tbn2, helptbn2, sticky="snew")
tkgrid.columnconfigure(tbn2,0,weight=10)
tkgrid.columnconfigure(helptbn2,0,weight=1)
insidetbn2 <- tkframe(tbn2)
tkpack(insidetbn2,fill='both',expand='yes')
scr2 <- tkscrollbar(insidetbn2, command=function(...)tkyview(txt2,...),bg='white')
txt2 <- tktext(insidetbn2,height=1, width=99,bg='grey')
xscr2 <- tkscrollbar(insidetbn2, command=function(...)tkxview(txt2,...),orient='horiz')
tkconfigure(txt2, yscrollcommand=function(...)tkset(scr2,...), xscrollcommand=function(...)tkset(xscr2,...), state="disabled")
tkpack(scr2,side='right',fill='y')
tkpack(txt2,expand='yes',fill='both')
tkpack(xscr2, side="bottom", fill="x")
sf <- tkcanvas(txt2, background="white")
tkwindow.create(txt2, 'end', window=sf)
cb1 <- tkcheckbutton(sf,command=function()check_allels(cbValu <- as.character(tclvalue(cbValuee)), cMtextEntryWidgetC, button.widget_co2, textEntryWidgetHC, textEntryWidgetH1C, textEntryWidgetH2C, textEntryWidgetH12C, textEntryWidgetHBC, textEntryWidgetH1BC, textEntryWidgetH2BC, textEntryWidgetH12BC), background="#FF6600")
if (length(con[which(con[,1]=="With Allels"),2]) > 0){
cbValuee <- tclVar(con[which(con[,1]=="With Allels"),2])
}else{
cbValuee <- tclVar("0")
}
tkconfigure(cb1,variable=cbValuee)
tkgrid(tklabel(sf,text="Analysis with more than one feature in data (aka HLA allels):", background="#FF6600"),cb1, sticky="snew", columnspan=1)
calc <- tkframe(sf,relief="groove",borderwidth=2)
sm <- tkframe(sf,relief="groove",borderwidth=2)
tkgrid(calc, sticky="snew")
tkgrid(sm, sticky="snew")
heading1 <- tklabel(calc,text="Discovering associations between mutation pairs and features", background="#FFCC99")
tkgrid(heading1, sticky="snew", columnspan=9)
button.widget_co1 <- tkbutton(calc,text="Select FASTA file",command=function()getFASTAfile(cMlabelText1, 2, 1))
cMlabelText <- tclVar("Sequence alignment to analyse *: ")
cMlabel1 <- tklabel(calc,text=tclvalue(cMlabelText))
tkconfigure(cMlabel1,textvariable=cMlabelText)
cMlabelText1 <- tclVar("")
cMlabel2 <- tklabel(calc,text=tclvalue(cMlabelText1))
tkconfigure(cMlabel2,textvariable=cMlabelText1)
tkgrid(cMlabel1, cMlabel2, button.widget_co1)
button.widget_co2 <- tkbutton(calc,text="Select FASTA file",command=function()getFASTAfile(cMlabelText1A, 2, 2))
tkconfigure(button.widget_co2, state="normal")
cMlabelTextA <- tclVar("Sequence consensus *: ")
cMlabel1A <- tklabel(calc,text=tclvalue(cMlabelTextA))
tkconfigure(cMlabel1A,textvariable=cMlabelTextA)
cMlabelText1A <- tclVar("")
cMlabel2A <- tklabel(calc,text=tclvalue(cMlabelText1A))
tkconfigure(cMlabel2A,textvariable=cMlabelText1A)
tkgrid(cMlabel1A, cMlabel2A, button.widget_co2)
cMlabelTextC <- tclVar("Minimal number of members *: ")
cMlabel1C <- tklabel(calc,text=tclvalue(cMlabelTextC))
if (length(con[which(con[,1]=="Number of patients threshold_cm"),2]) > 0){
cMtextEntryC <- tclVar(con[which(con[,1]=="Number of patients threshold_cm"),2])
}else{
cMtextEntryC <- tclVar("")
}
cMtextEntryWidgetC <- tkentry(calc,textvariable=cMtextEntryC)
tkconfigure(cMtextEntryWidgetC, state="disabled")
tkgrid(cMlabel1C, cMtextEntryWidgetC)
cMlabelTextD <- tclVar("Significance level *: ")
cMlabel1D <- tklabel(calc,text=tclvalue(cMlabelTextD))
if (length(con[which(con[,1]=="level for significance"),2]) > 0){
cMtextEntryD <- tclVar(con[which(con[,1]=="level for significance"),2])
}else{
cMtextEntryD <- tclVar("")
}
cMtextEntryWidgetD <- tkentry(calc,textvariable=cMtextEntryD)
tkgrid(cMlabel1D, cMtextEntryWidgetD)
cbm <- tkcheckbutton(calc)
if (length(con[which(con[,1]=="More than one core"),2]) > 0){
cbValuem <- tclVar(con[which(con[,1]=="More than one core"),2])
}else{
cbValuem <- tclVar("0")
}
tkconfigure(cbm,variable=cbValuem)
tkgrid(tklabel(calc,text="Use more than one core?"),cbm)
cMlabelTextHC <- tclVar("Position of feature A *: ")
cMlabel1HC <- tklabel(calc,text=tclvalue(cMlabelTextHC))
if (length(con[which(con[,1]=="cmHLA-A1"),2]) > 0){
textEntryHC <- tclVar(con[which(con[,1]=="cmHLA-A1"),2])
}else{
textEntryHC <- tclVar("")
}
textEntryWidgetHC <- tkentry(calc,width=3,textvariable=textEntryHC)
cMlabelTextH1C <- tclVar("-")
cMlabel1H1C <- tklabel(calc,text=tclvalue(cMlabelTextH1C))
if (length(con[which(con[,1]=="cmHLA-A2"),2]) > 0){
textEntryH1C <- tclVar(con[which(con[,1]=="cmHLA-A2"),2])
}else{
textEntryH1C <- tclVar("")
}
textEntryWidgetH1C <- tkentry(calc,width=3,textvariable=textEntryH1C)
if (length(con[which(con[,1]=="cmHLA-A3"),2]) > 0){
textEntryH2C <- tclVar(con[which(con[,1]=="cmHLA-A3"),2])
}else{
textEntryH2C <- tclVar("")
}
textEntryWidgetH2C <- tkentry(calc,width=3,textvariable=textEntryH2C)
cMlabelTextH12C <- tclVar("-")
cMlabel1H12C <- tklabel(calc,text=tclvalue(cMlabelTextH12C))
if (length(con[which(con[,1]=="cmHLA-A4"),2]) > 0){
textEntryH12C <- tclVar(con[which(con[,1]=="cmHLA-A4"),2])
}else{
textEntryH12C <- tclVar("")
}
textEntryWidgetH12C <- tkentry(calc,width=3,textvariable=textEntryH12C)
tkgrid(cMlabel1HC, textEntryWidgetHC, cMlabel1H1C, textEntryWidgetH1C, textEntryWidgetH2C, cMlabel1H12C, textEntryWidgetH12C)
tkconfigure(textEntryWidgetHC, state="disabled")
tkconfigure(textEntryWidgetH1C, state="disabled")
tkconfigure(textEntryWidgetH2C, state="disabled")
tkconfigure(textEntryWidgetH12C, state="disabled")
cMlabelTextHBC <- tclVar("Position of feature B *: ")
cMlabel1HBC <- tklabel(calc,text=tclvalue(cMlabelTextHBC))
if (length(con[which(con[,1]=="cmHLA-B1"),2]) > 0){
textEntryHBC <- tclVar(con[which(con[,1]=="cmHLA-B1"),2])
}else{
textEntryHBC <- tclVar("")
}
textEntryWidgetHBC <- tkentry(calc,width=3,textvariable=textEntryHBC)
cMlabelTextH1BC <- tclVar("-")
cMlabel1H1BC <- tklabel(calc,text=tclvalue(cMlabelTextH1BC))
if (length(con[which(con[,1]=="cmHLA-B2"),2]) > 0){
textEntryH1BC <- tclVar(con[which(con[,1]=="cmHLA-B2"),2])
}else{
textEntryH1BC <- tclVar("")
}
textEntryWidgetH1BC <- tkentry(calc,width=3,textvariable=textEntryH1BC)
if (length(con[which(con[,1]=="cmHLA-B3"),2]) > 0){
textEntryH2BC <- tclVar(con[which(con[,1]=="cmHLA-B3"),2])
}else{
textEntryH2BC <- tclVar("")
}
textEntryWidgetH2BC <- tkentry(calc,width=3,textvariable=textEntryH2BC)
cMlabelTextH12BC <- tclVar("-")
cMlabel1H12BC <- tklabel(calc,text=tclvalue(cMlabelTextH12BC))
if (length(con[which(con[,1]=="cmHLA-B4"),2]) > 0){
textEntryH12BC <- tclVar(con[which(con[,1]=="cmHLA-B4"),2])
}else{
textEntryH12BC <- tclVar("")
}
textEntryWidgetH12BC <- tkentry(calc,width=3,textvariable=textEntryH12BC)
tkgrid(cMlabel1HBC, textEntryWidgetHBC, cMlabel1H1BC, textEntryWidgetH1BC, textEntryWidgetH2BC, cMlabel1H12BC, textEntryWidgetH12BC)
tkconfigure(textEntryWidgetHBC, state="disabled")
tkconfigure(textEntryWidgetH1BC, state="disabled")
tkconfigure(textEntryWidgetH2BC, state="disabled")
tkconfigure(textEntryWidgetH12BC, state="disabled")
cmlabelTextIB <- tclVar("P-value correction *: ")
cmlabel1IB <- tklabel(calc,text=tclvalue(cmlabelTextIB))
ddbc <- tkframe(calc)
cmtextEntryIB <- tclVar()
dropdownList(ddbc, c("holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none"), cmtextEntryIB, 15, "none")
tkgrid(cmlabel1IB, ddbc)
OK.but21 <- tkbutton(calc,text="Start", foreground = "red",command=function()calculate_co_mut(cbVal <- as.character(tclvalue(cbValuee)), tbn2, txt, cMtextEntryC, cMtextEntryD, cmtextEntryIB, textEntryHC, textEntryH1C, textEntryH2C, textEntryH12C, textEntryHBC, textEntryH1BC, textEntryH2BC, textEntryH12BC, cmtextEntryIB, cbValue01))
tkgrid(OK.but21)
###set left:
tkgrid.configure(cMlabel1, sticky="w")
tkgrid.configure(cMlabel1A, sticky="w")
tkgrid.configure(cMlabel1C, sticky="w")
tkgrid.configure(cMlabel1D, sticky="w")
tkgrid.configure(cMlabel1HC, sticky="w")
tkgrid.configure(cMlabel1HBC, sticky="w")
tkgrid.configure(cmlabel1IB, sticky="w")
tkgrid.configure(button.widget_co1, column=8, sticky="e")
tkgrid.configure(button.widget_co2, column=8, sticky="e")
tkgrid.configure(OK.but21, column=8, sticky="e")
tkgrid.configure(cMlabel2, column=2, columnspan=6, sticky="w")
tkgrid.configure(cMlabel2A, column=2, columnspan=6, sticky="w")
tkgrid.configure(cMtextEntryWidgetC, column=2, columnspan=6)
tkgrid.configure(cMtextEntryWidgetD, column=2, columnspan=6)
tkgrid.configure(cbm, column=2, columnspan=6)
tkgrid.configure(ddbc, column=2, columnspan=6)
tkgrid.configure(textEntryWidgetHC, column=2)
tkgrid.configure(cMlabel1H1C, column=3)
tkgrid.configure(textEntryWidgetH1C, column=4)
tkgrid.configure(textEntryWidgetH2C, column=5)
tkgrid.configure(cMlabel1H12C, column=6)
tkgrid.configure(textEntryWidgetH12C, column=7)
tkgrid.configure(textEntryWidgetHBC, column=2)
tkgrid.configure(cMlabel1H1BC, column=3)
tkgrid.configure(textEntryWidgetH1BC, column=4)
tkgrid.configure(textEntryWidgetH2BC, column=5)
tkgrid.configure(cMlabel1H12BC, column=6)
tkgrid.configure(textEntryWidgetH12BC, column=7)
#-------------------------------
heading4 <- tklabel(sm,text="Discovering associations between n-tuple of mutations and features", background="#FFCC99")
tkgrid(heading4, sticky="snew", columnspan=9)
button.widget_sm1 <- tkbutton(sm,text="Select FASTA file",command=function()getFASTAfile(smlabelText1, 8, 1))
smlabelText <- tclVar("Sequence alignment to analyse: ")
smlabel1 <- tklabel(sm,text=tclvalue(smlabelText))
tkconfigure(smlabel1,textvariable=smlabelText)
smlabelText1 <- tclVar("")
smlabel12 <- tklabel(sm,text=tclvalue(smlabelText1))
tkconfigure(smlabel12,textvariable=smlabelText1)
tkgrid(smlabel1, smlabel12, button.widget_sm1)
button.widget_sm2 <- tkbutton(sm,text="Select csv file",command=function()getcsvfile(smlabelText3, 8, 2))
smlabelText2 <- tclVar("Results from \"point mutations\" *:")
smlabel2 <- tklabel(sm,text=tclvalue(smlabelText2))
tkconfigure(smlabel2,textvariable=smlabelText2)
smlabelText3 <- tclVar("")
smlabel3 <- tklabel(sm,text=tclvalue(smlabelText3))
tkconfigure(smlabel3,textvariable=smlabelText3)
tkgrid(smlabel2, smlabel3, button.widget_sm2)
smlabelTextA <- tclVar("Significance value *:")
smlabel1A <- tklabel(sm,text=tclvalue(smlabelTextA))
if (length(con[which(con[,1]=="threshold"),2]) > 0){
smtextEntryA <- tclVar(con[which(con[,1]=="threshold"),2])
}else{
smtextEntryA <- tclVar("")
}
smtextEntryWidgetA <- tkentry(sm,textvariable=smtextEntryA)
tkgrid(smlabel1A, smtextEntryWidgetA)
smlabelTextB <- tclVar("Min. nr. of elements in tuple *:")
smlabel1B <- tklabel(sm,text=tclvalue(smlabelTextB))
if (length(con[which(con[,1]=="min_number_of_ele_in_tupel"),2]) > 0){
smtextEntryB <- tclVar(con[which(con[,1]=="min_number_of_ele_in_tupel"),2])
}else{
smtextEntryB <- tclVar("")
}
smtextEntryWidgetB <- tkentry(sm,textvariable=smtextEntryB)
tkgrid(smlabel1B, smtextEntryWidgetB)
smlabelTextC <- tclVar("Max. nr. of elements in tuple *:")
smlabel1C <- tklabel(sm,text=tclvalue(smlabelTextC))
if (length(con[which(con[,1]=="max_number_of_ele_in_tuple"),2]) > 0){
smtextEntryC <- tclVar(con[which(con[,1]=="max_number_of_ele_in_tuple"),2])
}else{
smtextEntryC <- tclVar("")
}
smtextEntryWidgetC <- tkentry(sm,textvariable=smtextEntryC)
tkgrid(smlabel1C, smtextEntryWidgetC)
smlabelTextD <- tclVar("Column nr. of identifier *:")
smlabel1D <- tklabel(sm,text=tclvalue(smlabelTextD))
if (length(con[which(con[,1]=="column"),2]) > 0){
cbValue_0sM <- tclVar(con[which(con[,1]=="column"),2])
}else{
cbValue_0sM <- tclVar("")
}
smtextEntryWidgetD <- tkentry(sm,textvariable=cbValue_0sM)
tkgrid(smlabel1D, smtextEntryWidgetD)
smlabelTextD2 <- tclVar("Column nr. of alignment pos *:")
smlabel1D2 <- tklabel(sm,text=tclvalue(smlabelTextD2))
if (length(con[which(con[,1]=="column of position"),2]) > 0){
cbValue_0sM2 <- tclVar(con[which(con[,1]=="column of position"),2])
}else{
cbValue_0sM2 <- tclVar("")
}
smtextEntryWidgetD2 <- tkentry(sm,textvariable=cbValue_0sM2)
tkgrid(smlabel1D2, smtextEntryWidgetD2)
smlabelTextE <- tclVar("Column nr. of p-values *:")
smlabel1E <- tklabel(sm,text=tclvalue(smlabelTextE))
if (length(con[which(con[,1]=="column of values"),2]) > 0){
smtextEntryE <- tclVar(con[which(con[,1]=="column of values"),2])
}else{
smtextEntryE <- tclVar("")
}
smtextEntryWidgetE <- tkentry(sm,textvariable=smtextEntryE)
tkgrid(smlabel1E, smtextEntryWidgetE)
smlabelTextF <- tclVar("Column nr. of aa/nt *:")
smlabel1F <- tklabel(sm,text=tclvalue(smlabelTextF))
if (length(con[which(con[,1]=="column of aas"),2]) > 0){
smtextEntryF <- tclVar(con[which(con[,1]=="column of aas"),2])
}else{
smtextEntryF <- tclVar("")
}
smtextEntryWidgetF <- tkentry(sm,textvariable=smtextEntryF)
tkgrid(smlabel1F, smtextEntryWidgetF)
smlabelTextH <- tclVar("Position of feature A *:")
smlabel1H <- tklabel(sm,text=tclvalue(smlabelTextH))
if (length(con[which(con[,1]=="smHLA-A1"),2]) > 0){
smtextEntryH <- tclVar(con[which(con[,1]=="smHLA-A1"),2])
}else{
smtextEntryH <- tclVar("")
}
smtextEntryWidgetH <- tkentry(sm,width=3,textvariable=smtextEntryH)
smlabelTextH1 <- tclVar("-")
smlabel1H1 <- tklabel(sm,text=tclvalue(smlabelTextH1))
if (length(con[which(con[,1]=="smHLA-A2"),2]) > 0){
smtextEntryH1 <- tclVar(con[which(con[,1]=="smHLA-A2"),2])
}else{
smtextEntryH1 <- tclVar("")
}
smtextEntryWidgetH1 <- tkentry(sm,width=3,textvariable=smtextEntryH1)
if (length(con[which(con[,1]=="smHLA-A3"),2]) > 0){
smtextEntryH2 <- tclVar(con[which(con[,1]=="smHLA-A3"),2])
}else{
smtextEntryH2 <- tclVar("")
}
smtextEntryWidgetH2 <- tkentry(sm,width=3,textvariable=smtextEntryH2)
smlabelTextH12 <- tclVar("-")
smlabel1H12 <- tklabel(sm,text=tclvalue(smlabelTextH12))
if (length(con[which(con[,1]=="smHLA-A4"),2]) > 0){
smtextEntryH12 <- tclVar(con[which(con[,1]=="smHLA-A4"),2])
}else{
smtextEntryH12 <- tclVar("")
}
smtextEntryWidgetH12 <- tkentry(sm,width=3,textvariable=textEntryH12)
tkgrid(smlabel1H, smtextEntryWidgetH, smlabel1H1, smtextEntryWidgetH1, smtextEntryWidgetH2, smlabel1H12, smtextEntryWidgetH12)
smlabelTextHB <- tclVar("Position of feature B *:")
smlabel1HB <- tklabel(sm,text=tclvalue(smlabelTextHB))
if (length(con[which(con[,1]=="smHLA-B1"),2]) > 0){
smtextEntryHB <- tclVar(con[which(con[,1]=="smHLA-B1"),2])
}else{
smtextEntryHB <- tclVar("")
}
smtextEntryWidgetHB <- tkentry(sm,width=3,textvariable=smtextEntryHB)
smlabelTextH1B <- tclVar("-")
smlabel1H1B <- tklabel(sm,text=tclvalue(smlabelTextH1B))
if (length(con[which(con[,1]=="smHLA-B2"),2]) > 0){
smtextEntryH1B <- tclVar(con[which(con[,1]=="smHLA-B2"),2])
}else{
smtextEntryH1B <- tclVar("")
}
smtextEntryWidgetH1B <- tkentry(sm,width=3,textvariable=smtextEntryH1B)
if (length(con[which(con[,1]=="smHLA-B3"),2]) > 0){
smtextEntryH2B <- tclVar(con[which(con[,1]=="smHLA-B3"),2])
}else{
smtextEntryH2B <- tclVar("")
}
smtextEntryWidgetH2B <- tkentry(sm,width=3,textvariable=smtextEntryH2B)
smlabelTextH12B <- tclVar("-")
smlabel1H12B <- tklabel(sm,text=tclvalue(smlabelTextH12B))
if (length(con[which(con[,1]=="smHLA-B4"),2]) > 0){
smtextEntryH12B <- tclVar(con[which(con[,1]=="smHLA-B4"),2])
}else{
smtextEntryH12B <- tclVar("")
}
smtextEntryWidgetH12B <- tkentry(sm,width=3,textvariable=smtextEntryH12B)
tkgrid(smlabel1HB, smtextEntryWidgetHB, smlabel1H1B, smtextEntryWidgetH1B, smtextEntryWidgetH2B, smlabel1H12B, smtextEntryWidgetH12B)
smlabelTextX <- tclVar("Identifier (if only one feature): ")
smlabelX <- tklabel(sm,text=tclvalue(smlabelTextX))
if (length(con[which(con[,1]=="Identifier"),2]) > 0){
smtextEntryidet <- tclVar(con[which(con[,1]=="Identifier"),2])
}else{
smtextEntryidet <- tclVar("")
}
smtextEntryWidgetX <- tkentry(sm,textvariable=smtextEntryidet)
tkgrid(smlabelX, smtextEntryWidgetX)
tkconfigure(smtextEntryWidgetX, state="disabled")
OK.but4 <- tkbutton(sm,text="Start", foreground = "red",command=function()shared_mutations(tbn2, txt, smtextEntryA, smtextEntryB, smtextEntryC, cbValue_0sM, cbValue_0sM2, smtextEntryE, smtextEntryF, smtextEntryH, smtextEntryH1, smtextEntryH2, smtextEntryH12, smtextEntryHB, smtextEntryH1B, smtextEntryH2B, smtextEntryH12B, as.character(tclvalue(icbValue01)), smtextEntryidet ))
tkgrid(OK.but4)
###set left:
tkgrid.configure(smlabel1, sticky="w")
tkgrid.configure(smlabel2, sticky="w")
tkgrid.configure(smlabel1A, sticky="w")
tkgrid.configure(smlabel1B, sticky="w")
tkgrid.configure(smlabel1C, sticky="w")
tkgrid.configure(smlabel1D, sticky="w")
tkgrid.configure(smlabel1D2, sticky="w")
tkgrid.configure(smlabel1E, sticky="w")
tkgrid.configure(smlabel1F, sticky="w")
tkgrid.configure(smlabel1H, sticky="w")
tkgrid.configure(smlabel1HB, sticky="w")
tkgrid.configure(smlabelX, sticky="w")
tkgrid.configure(button.widget_sm1, column=8, sticky="e")
tkgrid.configure(button.widget_sm2, column=8, sticky="e")
tkgrid.configure(OK.but4, column=8, sticky="e")
tkgrid.configure(smlabel12, column=2, columnspan=6)
tkgrid.configure(smlabel3, column=2, columnspan=6)
tkgrid.configure(smtextEntryWidgetA, column=2, columnspan=6)
tkgrid.configure(smtextEntryWidgetB, column=2, columnspan=6)
tkgrid.configure(smtextEntryWidgetC, column=2, columnspan=6)
tkgrid.configure(smtextEntryWidgetD, column=2, columnspan=6)
tkgrid.configure(smtextEntryWidgetD2, column=2, columnspan=6)
tkgrid.configure(smtextEntryWidgetE, column=2, columnspan=6)
tkgrid.configure(smtextEntryWidgetF, column=2, columnspan=6)
tkgrid.configure(smtextEntryWidgetX, column=2, columnspan=6)
tkgrid.configure(smtextEntryWidgetH, column=2)
tkgrid.configure(smlabel1H1, column=3)
tkgrid.configure(smtextEntryWidgetH1, column=4)
tkgrid.configure(smtextEntryWidgetH2, column=5)
tkgrid.configure(smlabel1H12, column=6)
tkgrid.configure(smtextEntryWidgetH12, column=7)
tkgrid.configure(smtextEntryWidgetHB, column=2)
tkgrid.configure(smlabel1H1B, column=3)
tkgrid.configure(smtextEntryWidgetH1B, column=4)
tkgrid.configure(smtextEntryWidgetH2B, column=5)
tkgrid.configure(smlabel1H12B, column=6)
tkgrid.configure(smtextEntryWidgetH12B, column=7)
#--------------------------------------------------------------------------------------------------------------------------------
tkgrid.rowconfigure(otbn5,0,weight=1, minsize=100)
tkgrid.columnconfigure(otbn5,0,weight=10, minsize=200)
tkgrid.columnconfigure(otbn5,1,weight=3, minsize=100)
tbn5 <- ttkframe(otbn5)
helptbn5 <- ttkframe(otbn5)
tkgrid(tbn5, helptbn5, sticky="snew")
tkgrid.columnconfigure(tbn5,0,weight=10)
tkgrid.columnconfigure(helptbn5,0,weight=1)
scr3 <- tkscrollbar(tbn5, command=function(...)tkyview(txt3,...),bg='white')
txt3 <- tktext(tbn5,height=1,width=55,bg='grey')
xscr3 <- tkscrollbar(tbn5, command=function(...)tkxview(txt3,...),orient='horiz')
tkconfigure(txt3, yscrollcommand=function(...)tkset(scr3,...), xscrollcommand=function(...)tkset(xscr3,...), state="disabled")
tkpack(scr3,side='right',fill='y')
tkpack(txt3,expand='yes',fill='both')
tkpack(xscr3, side="bottom", fill="x")
sf3 <- tkcanvas(txt3, background="white")
tkwindow.create(txt3, 'end', window=sf3)
cb <- tkcheckbutton(sf3,command=function()check_allels(cbValu <- as.character(tclvalue(cbValue)), cMtextEntryWidgetC, button.widget_co2, textEntryWidgetHC, textEntryWidgetH1C, textEntryWidgetH2C, textEntryWidgetH12C, textEntryWidgetHBC, textEntryWidgetH1BC, textEntryWidgetH2BC, textEntryWidgetH12BC), background="#FF6600")
if (length(con[which(con[,1]=="cbWith Allels"),2]) > 0){
cbValue <- tclVar(con[which(con[,1]=="cbWith Allels"),2])
}else{
cbValue <- tclVar("0")
}
tkconfigure(cb,variable=cbValue)
tkgrid(tklabel(sf3,text="Analysis with more than one feature in data (aka HLA allels):", background="#FF6600"),cb, sticky="snew", columnspan=1)
graphicals <- tkframe(sf3,relief="groove",borderwidth=2)
graphicals2 <- tkframe(sf3,relief="groove",borderwidth=2)
tkgrid(graphicals, sticky="e")
tkgrid(graphicals2, sticky="snew")
#Co mutation graphics
heading2 <- tklabel(graphicals,text="Create graphics for n-tuple, one page per identifier", background="#FFCC99")
tkgrid(heading2, sticky="snew", columnspan=4)
button.widget_com <- tkbutton(graphicals,text="Select csv file",command=function()getcsvfile(cMlabelText1B, 5, 1))
cMlabelTextB <- tclVar("Result file from tuple analysis *:")
cMlabel1B <- tklabel(graphicals,text=tclvalue(cMlabelTextB))
tkconfigure(cMlabel1B,textvariable=cMlabelTextB)
cMlabelText1B <- tclVar("")
cMlabel2B <- tklabel(graphicals,text=tclvalue(cMlabelText1B))
tkconfigure(cMlabel2B,textvariable=cMlabelText1B)
tkgrid(cMlabel1B, cMlabel2B, button.widget_com)
cMlabelTextE <- tclVar("Significance level *:")
cMlabel1E <- tklabel(graphicals,text=tclvalue(cMlabelTextE))
if (length(con[which(con[,1]=="cMlevel for significance"),2]) > 0){
cMtextEntryE <- tclVar(con[which(con[,1]=="cMlevel for significance"),2])
}else{
cMtextEntryE <- tclVar("")
}
cMtextEntryWidgetE <- tkentry(graphicals,textvariable=cMtextEntryE)
tkgrid(cMlabel1E, cMtextEntryWidgetE)
OK.but22 <- tkbutton(graphicals, foreground = "red",text="Start",command=function()calculate_co_mut_graphics(cbVal2 <- as.character(tclvalue(cbValue)), tbn2, cMtextEntryE))
tkgrid(OK.but22)
###set left:
tkgrid.configure(cMlabel1B, sticky="w")
tkgrid.configure(cMlabel1E, sticky="w")
tkgrid.configure(cMlabel2B, column=2, sticky="w")
tkgrid.configure(cMtextEntryWidgetE, column=2)
tkgrid.configure(button.widget_com, column=3, sticky="e")
tkgrid.configure(OK.but22, column=3, sticky="e")
#double co mutation graphics
heading4 <- tklabel(graphicals2,text="Create tartan plot", background="#FFCC99")
tkgrid(heading4, sticky="snew", columnspan=4)
Tbutton.widget_com <- tkbutton(graphicals2,text="Select csv file",command=function()getcsvfile(TcMlabelText1B, 9, 1))
Tbutton.widget_com2 <- tkbutton(graphicals2,text="Select csv file",command=function()getcsvfile(TcMlabelText1B2, 9, 2))
Tbutton.widget_com3 <- tkbutton(graphicals2,text="Select csv file",command=function()getcsvfile(TcMlabelText1B3, 9, 3))
TcMlabelTextB <- tclVar("1st result from n-tuple vs. feature(s) *:")
TcMlabel1B <- tklabel(graphicals2,text=tclvalue(TcMlabelTextB))
tkconfigure(TcMlabel1B,textvariable=TcMlabelTextB)
TcMlabelText1B <- tclVar("")
TcMlabel2B <- tklabel(graphicals2,text=tclvalue(TcMlabelText1B))
tkconfigure(TcMlabel2B,textvariable=TcMlabelText1B)
tkgrid(TcMlabel1B, TcMlabel2B, Tbutton.widget_com)
TcMlabelTextB2 <- tclVar("2nd result from n-tuple vs. feature(s) *:")
TcMlabel1B2 <- tklabel(graphicals2,text=tclvalue(TcMlabelTextB2))
tkconfigure(TcMlabel1B2,textvariable=TcMlabelTextB2)
TcMlabelText1B2 <- tclVar("")
TcMlabel2B2 <- tklabel(graphicals2,text=tclvalue(TcMlabelText1B2))
tkconfigure(TcMlabel2B2,textvariable=TcMlabelText1B2)
tkgrid(TcMlabel1B2, TcMlabel2B2, Tbutton.widget_com2)
TcMlabelTextB3 <- tclVar("Optional: Distance matrix:")
TcMlabel1B3 <- tklabel(graphicals2,text=tclvalue(TcMlabelTextB3))
tkconfigure(TcMlabel1B3,textvariable=TcMlabelTextB3)
TcMlabelText1B3 <- tclVar("")
TcMlabel2B3 <- tklabel(graphicals2,text=tclvalue(TcMlabelText1B3))
tkconfigure(TcMlabel2B3,textvariable=TcMlabelText1B3)
tkgrid(TcMlabel1B3, TcMlabel2B3, Tbutton.widget_com3)
TcMlabelTextE <- tclVar("Optical space between blocks *:")
TcMlabel1E <- tklabel(graphicals2,text=tclvalue(TcMlabelTextE))
if (length(con[which(con[,1]=="space between blocks"),2]) > 0){
TcMtextEntryE <- tclVar(con[which(con[,1]=="space between blocks"),2])
}else{
TcMtextEntryE <- tclVar("")
}
TcMtextEntryWidgetE <- tkentry(graphicals2,textvariable=TcMtextEntryE)
tkgrid(TcMlabel1E, TcMtextEntryWidgetE)
TcMlabelTextE1 <- tclVar("Colors of the plot *:")
TcMlabel1E1 <- tklabel(graphicals2,text=tclvalue(TcMlabelTextE1))
if (length(con[which(con[,1]=="colors of the plot"),2]) > 0){
TcMtextEntryE1 <- tclVar(con[which(con[,1]=="colors of the plot"),2])
}else{
TcMtextEntryE1 <- tclVar("")
}
TcMtextEntryWidgetE1 <- tkentry(graphicals2,textvariable=TcMtextEntryE1)
tkgrid(TcMlabel1E1, TcMtextEntryWidgetE1)
TcMlabelTextE2 <- tclVar("x/y positions of added labels *:")
TcMlabel1E2 <- tklabel(graphicals2,text=tclvalue(TcMlabelTextE2))
if (length(con[which(con[,1]=="name positions"),2]) > 0){
TcMtextEntryE2 <- tclVar(con[which(con[,1]=="name positions"),2])
}else{
TcMtextEntryE2 <- tclVar("")
}
TcMtextEntryWidgetE2 <- tkentry(graphicals2,textvariable=TcMtextEntryE2)
tkgrid(TcMlabel1E2, TcMtextEntryWidgetE2)
TcMlabelTextE3 <- tclVar("Labelcontent *:")
TcMlabel1E3 <- tklabel(graphicals2,text=tclvalue(TcMlabelTextE3))
if (length(con[which(con[,1]=="names"),2]) > 0){
TcMtextEntryE3 <- tclVar(con[which(con[,1]=="names"),2])
}else{
TcMtextEntryE3 <- tclVar("")
}
TcMtextEntryWidgetE3 <- tkentry(graphicals2,textvariable=TcMtextEntryE3)
tkgrid(TcMlabel1E3, TcMtextEntryWidgetE3)
TcMlabelTextE4 <- tclVar("Ticks: ")
TcMlabel1E4 <- tklabel(graphicals2,text=tclvalue(TcMlabelTextE4))
if (length(con[which(con[,1]=="ticks"),2]) > 0){
TcMtextEntryE4 <- tclVar(con[which(con[,1]=="ticks"),2])
}else{
TcMtextEntryE4 <- tclVar("")
}
TcMtextEntryWidgetE4 <- tkentry(graphicals2,textvariable=TcMtextEntryE4)
tkgrid(TcMlabel1E4, TcMtextEntryWidgetE4)
TcMlabelTextE5 <- tclVar("Column nr. of 1st seq. pos. in 1st file *:")
TcMlabel1E5 <- tklabel(graphicals2,text=tclvalue(TcMlabelTextE5))
if (length(con[which(con[,1]=="column of first position in first file"),2]) > 0){
TcMtextEntryE5 <- tclVar(con[which(con[,1]=="column of first position in first file"),2])
}else{
TcMtextEntryE5 <- tclVar("")
}
TcMtextEntryWidgetE5 <- tkentry(graphicals2,textvariable=TcMtextEntryE5)
tkgrid(TcMlabel1E5, TcMtextEntryWidgetE5)
TcMlabelTextE6 <- tclVar("Column nr. of 2nd seq. pos. in 1st file *:")
TcMlabel1E6 <- tklabel(graphicals2,text=tclvalue(TcMlabelTextE6))
if (length(con[which(con[,1]=="column of second position in first file"),2]) > 0){
TcMtextEntryE6 <- tclVar(con[which(con[,1]=="column of second position in first file"),2])
}else{
TcMtextEntryE6 <- tclVar("")
}
TcMtextEntryWidgetE6 <- tkentry(graphicals2,textvariable=TcMtextEntryE6)
tkgrid(TcMlabel1E6, TcMtextEntryWidgetE6)
TcMlabelTextE7 <- tclVar("Column nr. of p-values in 1st file *:")
TcMlabel1E7 <- tklabel(graphicals2,text=tclvalue(TcMlabelTextE7))
if (length(con[which(con[,1]=="column of values in first file"),2]) > 0){
TcMtextEntryE7 <- tclVar(con[which(con[,1]=="column of values in first file"),2])
}else{
TcMtextEntryE7 <- tclVar("")
}
TcMtextEntryWidgetE7 <- tkentry(graphicals2,textvariable=TcMtextEntryE7)
tkgrid(TcMlabel1E7, TcMtextEntryWidgetE7)
TcMlabelTextE8 <- tclVar("Column nr. of 1st seq. pos. in 2nd file *:")
TcMlabel1E8 <- tklabel(graphicals2,text=tclvalue(TcMlabelTextE8))
if (length(con[which(con[,1]=="column of first position in second file"),2]) > 0){
TcMtextEntryE8 <- tclVar(con[which(con[,1]=="column of first position in second file"),2])
}else{
TcMtextEntryE8 <- tclVar("")
}
TcMtextEntryWidgetE8 <- tkentry(graphicals2,textvariable=TcMtextEntryE8)
tkgrid(TcMlabel1E8, TcMtextEntryWidgetE8)
TcMlabelTextE9 <- tclVar("Column nr. of 2nd seq. pos. in 2nd file *:")
TcMlabel1E9 <- tklabel(graphicals2,text=tclvalue(TcMlabelTextE9))
if (length(con[which(con[,1]=="column of second position in second file"),2]) > 0){
TcMtextEntryE9 <- tclVar(con[which(con[,1]=="column of second position in second file"),2])
}else{
TcMtextEntryE9 <- tclVar("")
}
TcMtextEntryWidgetE9 <- tkentry(graphicals2,textvariable=TcMtextEntryE9)
tkgrid(TcMlabel1E9, TcMtextEntryWidgetE9)
TcMlabelTextE0 <- tclVar("Column nr. of p-values in 2nd file *:")
TcMlabel1E0 <- tklabel(graphicals2,text=tclvalue(TcMlabelTextE0))
if (length(con[which(con[,1]=="column of values in second file"),2]) > 0){
TcMtextEntryE0 <- tclVar(con[which(con[,1]=="column of values in second file"),2])
}else{
TcMtextEntryE0 <- tclVar("")
}
TcMtextEntryWidgetE0 <- tkentry(graphicals2,textvariable=TcMtextEntryE0)
tkgrid(TcMlabel1E0, TcMtextEntryWidgetE0)
TOK.but22 <- tkbutton(graphicals2, foreground = "red",text="Start",command=function()calculate_co_mut_graphics_both(tbn5, txt, TcMtextEntryE, TcMtextEntryE1, TcMtextEntryE2, TcMtextEntryE3, TcMtextEntryE4, TcMtextEntryE5, TcMtextEntryE6, TcMtextEntryE7, TcMtextEntryE8, TcMtextEntryE9, TcMtextEntryE0))
tkgrid(TOK.but22)
###set left:
tkgrid.configure(TcMlabel1B, sticky="w")
tkgrid.configure(TcMlabel1B2, sticky="w")
tkgrid.configure(TcMlabel1B3, sticky="w")
tkgrid.configure(TcMlabel1E, sticky="w")
tkgrid.configure(TcMlabel1E1, sticky="w")
tkgrid.configure(TcMlabel1E2, sticky="w")
tkgrid.configure(TcMlabel1E3, sticky="w")
tkgrid.configure(TcMlabel1E4, sticky="w")
tkgrid.configure(TcMlabel1E5, sticky="w")
tkgrid.configure(TcMlabel1E6, sticky="w")
tkgrid.configure(TcMlabel1E7, sticky="w")
tkgrid.configure(TcMlabel1E8, sticky="w")
tkgrid.configure(TcMlabel1E9, sticky="w")
tkgrid.configure(TcMlabel1E0, sticky="w")
tkgrid.configure(TcMlabel2B, column=2, sticky="w")
tkgrid.configure(TcMlabel2B2, column=2, sticky="w")
tkgrid.configure(TcMtextEntryWidgetE, column=2)
tkgrid.configure(TcMtextEntryWidgetE1, column=2)
tkgrid.configure(TcMtextEntryWidgetE2, column=2)
tkgrid.configure(TcMtextEntryWidgetE3, column=2)
tkgrid.configure(TcMtextEntryWidgetE4, column=2)
tkgrid.configure(TcMtextEntryWidgetE5, column=2)
tkgrid.configure(TcMtextEntryWidgetE6, column=2)
tkgrid.configure(TcMtextEntryWidgetE7, column=2)
tkgrid.configure(TcMtextEntryWidgetE8, column=2)
tkgrid.configure(TcMtextEntryWidgetE9, column=2)
tkgrid.configure(TcMtextEntryWidgetE0, column=2)
tkgrid.configure(Tbutton.widget_com, column=3, sticky="e")
tkgrid.configure(Tbutton.widget_com2, column=3, sticky="e")
tkgrid.configure(Tbutton.widget_com3, column=3, sticky="e")
tkgrid.configure(TOK.but22, column=3, sticky="e")
#--------------------------------------------------------------------------------------------------------------------------------
tkgrid.rowconfigure(otbn3,0,weight=1, minsize=100)
tkgrid.columnconfigure(otbn3,0,weight=10, minsize=100)
tkgrid.columnconfigure(otbn3,1,weight=3, minsize=100)
tbn3 <- ttkframe(otbn3)
helptbn3 <- ttkframe(otbn3)
tkgrid(tbn3, helptbn3, sticky="snew")
tkgrid.columnconfigure(tbn3,0,weight=10)
tkgrid.columnconfigure(helptbn3,0,weight=1)
scr5 <- tkscrollbar(tbn3, command=function(...)tkyview(txt5,...),bg='white')
txt5 <- tktext(tbn3,height=1,width=5,bg='grey')
xscr5 <- tkscrollbar(tbn3, command=function(...)tkxview(txt5,...),orient='horiz')
tkconfigure(txt5, yscrollcommand=function(...)tkset(scr5,...), xscrollcommand=function(...)tkset(xscr5,...), state="disabled")
tkpack(scr5,side='right',fill='y')
tkpack(txt5,expand='yes',fill='both')
tkpack(xscr5, side="bottom", fill="x")
sf3 <- tkcanvas(txt5, background="white")
tkwindow.create(txt5,'end', window=sf3)
# small manhattan
sMA <- tkframe(sf3,relief="groove",borderwidth=2)
tkgrid(sMA, sticky="e")
headingsMA <- tklabel(sMA,text="Small manhattan plot", background="#FFCC99")
tkgrid(headingsMA, sticky="snew", columnspan=5)
button.widget_epi1 <- tkbutton(sMA,text="Select csv file",command=function()getcsvfile(sMAlabelText1, 12, 1))
sMAlabelText <- tclVar("Result from assoc point *: ")
sMAlabel1 <- tklabel(sMA,text=tclvalue(sMAlabelText))
tkconfigure(sMAlabel1,textvariable=sMAlabelText)
sMAlabelText1 <- tclVar("")
sMAlabel2 <- tklabel(sMA,text=tclvalue(sMAlabelText1))
tkconfigure(sMAlabel2,textvariable=sMAlabelText1)
tkgrid(sMAlabel1, sMAlabel2, button.widget_epi1)
sMAlabelTextC <- tclVar("Feature *: ")
sMAlabel1C <- tklabel(sMA,text=tclvalue(sMAlabelTextC))
if (length(con[which(con[,1]=="Feat"),2]) > 0){
sMAtextEntryC <- tclVar(con[which(con[,1]=="Feat"),2])
}else{
sMAtextEntryC <- tclVar("")
}
sMAtextEntryWidgetC <- tkentry(sMA,textvariable=sMAtextEntryC)
tkgrid(sMAlabel1C, sMAtextEntryWidgetC)
cb0sMA <- tkcheckbutton(sMA)
if (length(con[which(con[,1]=="corrected"),2]) > 0){
cbValue_0sMA <- tclVar(con[which(con[,1]=="corrected"),2])
}else{
cbValue_0sMA <- tclVar("0")
}
tkconfigure(cb0sMA,variable=cbValue_0sMA)
tkgrid(tklabel(sMA,text="Use corrected values?"),cb0sMA, sticky="snew")
sMAlabelTextF <- tclVar("x-axis-breaks *: ")
sMAlabel1F <- tklabel(sMA,text=tclvalue(sMAlabelTextF))
if (length(con[which(con[,1]=="axis_breaks"),2]) > 0){
sMAtextEntryF <- tclVar(con[which(con[,1]=="axis_breaks"),2])
}else{
sMAtextEntryF <- tclVar("")
}
sMAtextEntryWidgetF <- tkentry(sMA,textvariable=sMAtextEntryF)
tkgrid(sMAlabel1F, sMAtextEntryWidgetF)
OK.butsMA <- tkbutton(sMA,text="Start", foreground = "red",command=function()small_manhattan(tbn3, sMAtextEntryC, cbValue_0sMA, sMAtextEntryF, txt))
tkgrid(OK.butsMA)
###set left:
tkgrid.configure(sMAlabel1, sticky="w")
tkgrid.configure(sMAlabel1C, sticky="w")
tkgrid.configure(sMAlabel1F, sticky="w")
tkgrid.configure(sMAlabel2, column=2, columnspan=2, sticky="w")
tkgrid.configure(sMAtextEntryWidgetC, column=2, columnspan=2)
tkgrid.configure(sMAtextEntryWidgetF, column=2, columnspan=2)
tkgrid.configure(cb0sMA, column=2, columnspan=6)
tkgrid.configure(OK.butsMA, column=4, sticky="e")
tkgrid.configure(button.widget_epi1, column=4, sticky="e")
#Get frequencies###-----------------------
gF <- tkframe(sf3,relief="groove",borderwidth=2)
tkgrid(gF, sticky="snew")
headinggf <- tklabel(gF,text="Get frequencys for epitopes", background="#FFCC99")
tkgrid(headinggf, sticky="snew", columnspan=9)
button.widget_epi1 <- tkbutton(gF,text="Select FASTA file",command=function()getFASTAfile(gFlabelText1, 11, 1))
gFlabelText <- tclVar("Sequence alignment to analyse *: ")
gFlabel1 <- tklabel(gF,text=tclvalue(gFlabelText))
tkconfigure(gFlabel1,textvariable=gFlabelText)
gFlabelText1 <- tclVar("")
gFlabel2 <- tklabel(gF,text=tclvalue(gFlabelText1))
tkconfigure(gFlabel2,textvariable=gFlabelText1)
tkgrid(gFlabel1, gFlabel2, button.widget_epi1)
button.widget_epi12 <- tkbutton(gF,text="Select FASTA file",command=function()getFASTAfile(gFlabelText12, 11, 2))
gFlabelText2 <- tclVar("Sequence consensus*: ")
gFlabel12 <- tklabel(gF,text=tclvalue(gFlabelText2))
tkconfigure(gFlabel12,textvariable=gFlabelText2)
gFlabelText12 <- tclVar("")
gFlabel22 <- tklabel(gF,text=tclvalue(gFlabelText12))
tkconfigure(gFlabel22,textvariable=gFlabelText12)
tkgrid(gFlabel12, gFlabel22, button.widget_epi12)
gFlabelTextC <- tclVar("Starting pos. of epitope in alignment *: ")
gFlabel1C <- tklabel(gF,text=tclvalue(gFlabelTextC))
if (length(con[which(con[,1]=="Epi start"),2]) > 0){
gFtextEntryC <- tclVar(con[which(con[,1]=="Epi start"),2])
}else{
gFtextEntryC <- tclVar("")
}
gFtextEntryWidgetC <- tkentry(gF,textvariable=gFtextEntryC)
tkgrid(gFlabel1C, gFtextEntryWidgetC)
gFlabelTextD <- tclVar("Ending pos. of epitope in alignment *: ")
gFlabel1D <- tklabel(gF,text=tclvalue(gFlabelTextD))
if (length(con[which(con[,1]=="Epi end"),2]) > 0){
gFtextEntryD <- tclVar(con[which(con[,1]=="Epi end"),2])
}else{
gFtextEntryD <- tclVar("")
}
gFtextEntryWidgetD <- tkentry(gF,textvariable=gFtextEntryD)
tkgrid(gFlabel1D, gFtextEntryWidgetD)
gFlabelTextF <- tclVar("Minimal number of members *: ")
gFlabel1F <- tklabel(gF,text=tclvalue(gFlabelTextF))
if (length(con[which(con[,1]=="Number of patients threshold"),2]) > 0){
gFtextEntryF <- tclVar(con[which(con[,1]=="Number of patients threshold"),2])
}else{
gFtextEntryF <- tclVar("")
}
gFtextEntryWidgetF <- tkentry(gF,textvariable=gFtextEntryF)
tkgrid(gFlabel1F, gFtextEntryWidgetF)
gFlabelTextH <- tclVar("Position of feature A *: ")
gFlabel1H <- tklabel(gF,text=tclvalue(gFlabelTextH))
if (length(con[which(con[,1]=="gfgF_HLA-A1"),2]) > 0){
gFtextEntryH <- tclVar(con[which(con[,1]=="gF_HLA-A1"),2])
}else{
gFtextEntryH <- tclVar("")
}
gFtextEntryWidgetH <- tkentry(gF,width=3,textvariable=gFtextEntryH)
gFlabelTextH1 <- tclVar("-")
gFlabel1H1 <- tklabel(gF,text=tclvalue(gFlabelTextH1))
if (length(con[which(con[,1]=="gF_HLA-A2"),2]) > 0){
gFtextEntryH1 <- tclVar(con[which(con[,1]=="gF_HLA-A2"),2])
}else{
gFtextEntryH1 <- tclVar("")
}
gFtextEntryWidgetH1 <- tkentry(gF,width=3,textvariable=gFtextEntryH1)
if (length(con[which(con[,1]=="gF_HLA-A3"),2]) > 0){
gFtextEntryH2 <- tclVar(con[which(con[,1]=="gF_HLA-A3"),2])
}else{
gFtextEntryH2 <- tclVar("")
}
gFtextEntryWidgetH2 <- tkentry(gF,width=3,textvariable=gFtextEntryH2)
gFlabelTextH12 <- tclVar("-")
gFlabel1H12 <- tklabel(gF,text=tclvalue(gFlabelTextH12))
if (length(con[which(con[,1]=="gF_HLA-A4"),2]) > 0){
gFtextEntryH12 <- tclVar(con[which(con[,1]=="gF_HLA-A4"),2])
}else{
gFtextEntryH12 <- tclVar("")
}
gFtextEntryWidgetH12 <- tkentry(gF,width=3,textvariable=gFtextEntryH12)
tkgrid(gFlabel1H, gFtextEntryWidgetH, gFlabel1H1, gFtextEntryWidgetH1, gFtextEntryWidgetH2, gFlabel1H12, gFtextEntryWidgetH12)
gFlabelTextHB <- tclVar("Position of feature B *: ")
gFlabel1HB <- tklabel(gF,text=tclvalue(gFlabelTextHB))
if (length(con[which(con[,1]=="gF_HLA-B1"),2]) > 0){
gFtextEntryHB <- tclVar(con[which(con[,1]=="gF_HLA-B1"),2])
}else{
gFtextEntryHB <- tclVar("")
}
gFtextEntryWidgetHB <- tkentry(gF,width=3,textvariable=gFtextEntryHB)
gFlabelTextH1B <- tclVar("-")
gFlabel1H1B <- tklabel(gF,text=tclvalue(gFlabelTextH1B))
if (length(con[which(con[,1]=="gF_HLA-B2"),2]) > 0){
gFtextEntryH1B <- tclVar(con[which(con[,1]=="gF_HLA-B2"),2])
}else{
gFtextEntryH1B <- tclVar("")
}
gFtextEntryWidgetH1B <- tkentry(gF,width=3,textvariable=gFtextEntryH1B)
if (length(con[which(con[,1]=="gF_HLA-B3"),2]) > 0){
gFtextEntryH2B <- tclVar(con[which(con[,1]=="gF_HLA-B3"),2])
}else{
gFtextEntryH2B <- tclVar("")
}
gFtextEntryWidgetH2B <- tkentry(gF,width=3,textvariable=gFtextEntryH2B)
gFlabelTextH12B <- tclVar("-")
gFlabel1H12B <- tklabel(gF,text=tclvalue(gFlabelTextH12B))
if (length(con[which(con[,1]=="gF_HLA-B4"),2]) > 0){
gFtextEntryH12B <- tclVar(con[which(con[,1]=="gF_HLA-B4"),2])
}else{
gFtextEntryH12B <- tclVar("")
}
gFtextEntryWidgetH12B <- tkentry(gF,width=3,textvariable=gFtextEntryH12B)
tkgrid(gFlabel1HB, gFtextEntryWidgetHB, gFlabel1H1B, gFtextEntryWidgetH1B, gFtextEntryWidgetH2B, gFlabel1H12B, gFtextEntryWidgetH12B)
OK.but10 <- tkbutton(gF,text="Start", foreground = "red",command=function()get_freqs(tbn3, gFtextEntryC, gFtextEntryD, gFtextEntryF, gFtextEntryH, gFtextEntryH1, gFtextEntryH2, gFtextEntryH12, gFtextEntryHB, gFtextEntryH1B, gFtextEntryH2B, gFtextEntryH12B, txt))
tkgrid(OK.but10)
###set left:
tkgrid.configure(gFlabel1, sticky="w")
tkgrid.configure(gFlabel12, sticky="w")
tkgrid.configure(gFlabel1C, sticky="w")
tkgrid.configure(gFlabel1D, sticky="w")
tkgrid.configure(gFlabel1F, sticky="w")
tkgrid.configure(gFlabel1H, sticky="w")
tkgrid.configure(gFlabel1HB, sticky="w")
tkgrid.configure(gFlabel2, column=2, columnspan=6, sticky="w")
tkgrid.configure(gFlabel22, column=2, columnspan=6, sticky="w")
tkgrid.configure(gFtextEntryWidgetC, column=2, columnspan=6)
tkgrid.configure(gFtextEntryWidgetD, column=2, columnspan=6)
tkgrid.configure(gFtextEntryWidgetF, column=2, columnspan=6)
tkgrid.configure(button.widget_epi1, column=8, sticky="e")
tkgrid.configure(button.widget_epi12, column=8, sticky="e")
tkgrid.configure(OK.but10, column=8, sticky="e")
tkgrid.configure(gFtextEntryWidgetH, column=2)
tkgrid.configure(gFlabel1H1, column=3)
tkgrid.configure(gFtextEntryWidgetH1, column=4)
tkgrid.configure(gFtextEntryWidgetH2, column=5)
tkgrid.configure(gFlabel1H12, column=6)
tkgrid.configure(gFtextEntryWidgetH12, column=7)
tkgrid.configure(gFtextEntryWidgetHB, column=2)
tkgrid.configure(gFlabel1H1B, column=3)
tkgrid.configure(gFtextEntryWidgetH1B, column=4)
tkgrid.configure(gFtextEntryWidgetH2B, column=5)
tkgrid.configure(gFlabel1H12B, column=6)
tkgrid.configure(gFtextEntryWidgetH12B, column=7)
#----------------------------------------------------------------
qv <- tkframe(sf3,relief="groove",borderwidth=2)
tkgrid(qv, sticky="e")
heading4 <- tklabel(qv,text="Calculate q-values from p-values", background="#FFCC99")
tkgrid(heading4, sticky="snew", columnspan=4)
button.widget_q <- tkbutton(qv,text="Select csv file",command=function()getcsvfile(qVlabelText1, 3, 1))
qVlabelText <- tclVar("csv file *:")
qVlabel1 <- tklabel(qv,text=tclvalue(qVlabelText))
tkconfigure(qVlabel1,textvariable=qVlabelText)
qVlabelText1 <- tclVar("")
qVlabel2 <- tklabel(qv,text=tclvalue(qVlabelText1))
tkconfigure(qVlabel2,textvariable=qVlabelText1)
tkgrid(qVlabel1, qVlabel2, button.widget_q)
OK.but3 <- tkbutton(qv,text="Start", foreground = "red",command=function()calculate_q_value(tbn3, txt))
tkgrid(OK.but3)
###set left:
tkgrid.configure(qVlabel1, sticky="w")
tkgrid.configure(qVlabel2, column=2, sticky="w")
tkgrid.configure(button.widget_q, column=3, sticky="e")
tkgrid.configure(OK.but3, column=3, sticky="e")
#---------------------------------------------------------
epa <- tkframe(sf3,relief="groove",borderwidth=2)
tkgrid(epa, sticky="e")
heading <- tklabel(epa,text="Combine results of point and tuple mutations", background="#FFCC99")
tkgrid(heading, sticky="snew", columnspan=4)
button.widget_epa1 <- tkbutton(epa,text="Select FASTA file",command=function()getFASTAfile(pEFlabelText1, 4, 1))
pEFlabelText <- tclVar("Sequence alignment to analyse *:")
pEFlabel1 <- tklabel(epa,text=tclvalue(pEFlabelText))
tkconfigure(pEFlabel1,textvariable=pEFlabelText)
pEFlabelText1 <- tclVar("")
pEFlabel2 <- tklabel(epa,text=tclvalue(pEFlabelText1))
tkconfigure(pEFlabel2,textvariable=pEFlabelText1)
tkgrid(pEFlabel1, pEFlabel2, button.widget_epa1)
button.widget_epa2 <- tkbutton(epa,text="Select csv file",command=function()getcsvfile(pEFlabelText1A, 4, 2))
pEFlabelTextA <- tclVar("Result file from point mutations *:")
pEFlabel1A <- tklabel(epa,text=tclvalue(pEFlabelTextA))
tkconfigure(pEFlabel1A,textvariable=pEFlabelTextA)
pEFlabelText1A <- tclVar("")
pEFlabel2A <- tklabel(epa,text=tclvalue(pEFlabelText1A))
tkconfigure(pEFlabel2A,textvariable=pEFlabelText1A)
tkgrid(pEFlabel1A, pEFlabel2A, button.widget_epa2)
button.widget_epa3 <- tkbutton(epa,text="Select csv file",command=function()getcsvfile(pEFlabelText1B, 4, 3))
pEFlabelTextB <- tclVar("Result file from tuple mutations *:")
pEFlabel1B <- tklabel(epa,text=tclvalue(pEFlabelTextB))
tkconfigure(pEFlabel1B,textvariable=pEFlabelTextB)
pEFlabelText1B <- tclVar("")
pEFlabel2B <- tklabel(epa,text=tclvalue(pEFlabelText1B))
tkconfigure(pEFlabel2B,textvariable=pEFlabelText1B)
tkgrid(pEFlabel1B, pEFlabel2B, button.widget_epa3)
pElabelText2 <- tclVar("p-value *:")
pElabel2G <- tklabel(epa,text=tclvalue(pElabelText2))
if (length(con[which(con[,1]=="p-value addon"),2]) > 0){
textEntry_p.value <- tclVar(con[which(con[,1]=="p-value addon"),2])
}else{
textEntry_p.value <- tclVar("")
}
textEntry_Wp.value <- tkentry(epa,textvariable=textEntry_p.value)
tkgrid(pElabel2G, textEntry_Wp.value)
OK.bute2 <- tkbutton(epa,text="Start", foreground = "red",command=function()calculate_pos_epi_further(tbn3, textEntry_p.value, txt))
tkgrid(OK.bute2)
###set left:
tkgrid.configure(pEFlabel1, sticky="w")
tkgrid.configure(pEFlabel1A, sticky="w")
tkgrid.configure(pEFlabel1B, sticky="w")
tkgrid.configure(pElabel2G, sticky="w")
tkgrid.configure(pEFlabel2, column=2, sticky="w")
tkgrid.configure(pEFlabel2A, column=2, sticky="w")
tkgrid.configure(pEFlabel2B, column=2, sticky="w")
tkgrid.configure(textEntry_Wp.value, sticky="w")
tkgrid.configure(button.widget_epa1, column=3, sticky="e")
tkgrid.configure(button.widget_epa2, column=3, sticky="e")
tkgrid.configure(button.widget_epa3, column=3, sticky="e")
tkgrid.configure(OK.bute2, column=3, sticky="e")
#-----------------------------------------------------
#Founder elem
fe <- tkframe(sf3,relief="groove",borderwidth=2)
tkgrid(fe, sticky="e")
heading3 <- tklabel(fe,text="Founder effect finder", background="#FFCC99")
tkgrid(heading3, sticky="snew", columnspan=4)
button.widget_fe1 <- tkbutton(fe,text="Select FASTA file",command=function()getFASTAfile(felabelText1, 6, 1))
felabelText <- tclVar("Sequence alignment to analyse *:")
felabel1 <- tklabel(fe,text=tclvalue(felabelText))
tkconfigure(felabel1,textvariable=felabelText)
felabelText1 <- tclVar("")
felabel2 <- tklabel(fe,text=tclvalue(felabelText1))
tkconfigure(felabel2,textvariable=felabelText1)
tkgrid(felabel1, felabel2, button.widget_fe1)
button.widget_fe2 <- tkbutton(fe,text="Select csv file",command=function()getcsvfile(felabelText12, 6, 2))
felabelText2 <- tclVar("Result file from tuple mutations *:")
felabel12 <- tklabel(fe,text=tclvalue(felabelText2))
tkconfigure(felabel12,textvariable=felabelText2)
felabelText12 <- tclVar("")
felabel22 <- tklabel(fe,text=tclvalue(felabelText12))
tkconfigure(felabel22,textvariable=felabelText12)
tkgrid(felabel12, felabel22, button.widget_fe2)
button.widget_fe3 <- tkbutton(fe,text="Select nexus file",command=function()getnexusfile(felabelText13, 6, 3))
felabelText3 <- tclVar("Tree file *:")
felabel13 <- tklabel(fe,text=tclvalue(felabelText3))
tkconfigure(felabel13,textvariable=felabelText3)
felabelText13 <- tclVar("")
felabel23 <- tklabel(fe,text=tclvalue(felabelText13))
tkconfigure(felabel23,textvariable=felabelText13)
tkgrid(felabel13, felabel23, button.widget_fe3)
felabelTextE <- tclVar("Ratio in subtree *:")
felabel1E <- tklabel(fe,text=tclvalue(felabelTextE))
if (length(con[which(con[,1]=="Ratio in subtree"),2]) > 0){
fetextEntryE <- tclVar(con[which(con[,1]=="Ratio in subtree"),2])
}else{
fetextEntryE <- tclVar("")
}
fetextEntryWidgetE <- tkentry(fe,width=20,textvariable=fetextEntryE)
tkgrid(felabel1E, fetextEntryWidgetE)
OK.but62 <- tkbutton(fe,text="Start", foreground = "red",command=function()calculate_founder(tbn3, fetextEntryE, txt))
tkgrid(OK.but62)
###set left:
tkgrid.configure(felabel1, sticky="w")
tkgrid.configure(felabel12, sticky="w")
tkgrid.configure(felabel13, sticky="w")
tkgrid.configure(felabel1E, sticky="w")
tkgrid.configure(felabel2, column=2, sticky="w")
tkgrid.configure(felabel22, column=2, sticky="w")
tkgrid.configure(felabel23, column=2, sticky="w")
tkgrid.configure(fetextEntryWidgetE, column=2, sticky="w")
tkgrid.configure(button.widget_fe1, column=3, sticky="e")
tkgrid.configure(button.widget_fe2, column=3, sticky="e")
tkgrid.configure(button.widget_fe3, column=3, sticky="e")
tkgrid.configure(OK.but62, column=3, sticky="e")
#### Rewrite shared mutations----------------------------
rsm <- tkframe(sf3,relief="groove",borderwidth=2)
tkgrid(rsm, sticky="e")
heading3 <- tklabel(rsm,text="Rewrite tuple analysis result for tartan", background="#FFCC99")
tkgrid(heading3, sticky="snew", columnspan=4)
button.widget_rsm2 <- tkbutton(rsm,text="Select csv file",command=function()getcsvfile(rsmlabelText12, 10, 1))
rsmlabelText2 <- tclVar("Result file from tuple analysis *:")
rsmlabel12 <- tklabel(rsm,text=tclvalue(rsmlabelText2))
tkconfigure(rsmlabel12,textvariable=rsmlabelText2)
rsmlabelText12 <- tclVar("")
rsmlabel22 <- tklabel(rsm,text=tclvalue(rsmlabelText12))
tkconfigure(rsmlabel22,textvariable=rsmlabelText12)
tkgrid(rsmlabel12, rsmlabel22, button.widget_rsm2)
rsmlabelTextE5 <- tclVar("Column of 1st sequence position *:")
rsmlabel1E5 <- tklabel(rsm,text=tclvalue(rsmlabelTextE5))
if (length(con[which(con[,1]=="rw column of first position"),2]) > 0){
rsmtextEntryE5 <- tclVar(con[which(con[,1]=="rw column of first position"),2])
}else{
rsmtextEntryE5 <- tclVar("")
}
rsmtextEntryWidgetE5 <- tkentry(rsm,textvariable=rsmtextEntryE5)
tkgrid(rsmlabel1E5, rsmtextEntryWidgetE5)
rsmlabelTextE6 <- tclVar("Column of 2nd sequence position *:")
rsmlabel1E6 <- tklabel(rsm,text=tclvalue(rsmlabelTextE6))
if (length(con[which(con[,1]=="rw column of second position"),2]) > 0){
rsmtextEntryE6 <- tclVar(con[which(con[,1]=="rw column of second position"),2])
}else{
rsmtextEntryE6 <- tclVar("")
}
rsmtextEntryWidgetE6 <- tkentry(rsm,textvariable=rsmtextEntryE6)
tkgrid(rsmlabel1E6, rsmtextEntryWidgetE6)
rsmlabelTextE7 <- tclVar("Column of p-values *:")
rsmlabel1E7 <- tklabel(rsm,text=tclvalue(rsmlabelTextE7))
if (length(con[which(con[,1]=="rw column of values"),2]) > 0){
rsmtextEntryE7 <- tclVar(con[which(con[,1]=="rw column of values"),2])
}else{
rsmtextEntryE7 <- tclVar("")
}
rsmtextEntryWidgetE7 <- tkentry(rsm,textvariable=rsmtextEntryE7)
tkgrid(rsmlabel1E7, rsmtextEntryWidgetE7)
rsmlabelTextA <- tclVar("csv seperator *:")
rsmlabel1A <- tklabel(rsm,text=tclvalue(rsmlabelTextA))
if (length(con[which(con[,1]=="rw csv seperator"),2]) > 0){
rsmtextEntryA <- tclVar(con[which(con[,1]=="rw csv seperator"),2])
}else{
rsmtextEntryA <- tclVar("")
}
rsmtextEntryWidgetA <- tkentry(rsm,textvariable=rsmtextEntryA)
tkgrid(rsmlabel1A, rsmtextEntryWidgetA)
rsmlabelTextB <- tclVar("Significance value *:")
rsmlabel1B <- tklabel(rsm,text=tclvalue(rsmlabelTextB))
if (length(con[which(con[,1]=="rw threshold"),2]) > 0){
rsmtextEntryB <- tclVar(con[which(con[,1]=="rw threshold"),2])
}else{
rsmtextEntryB <- tclVar("")
}
rsmtextEntryWidgetB <- tkentry(rsm,textvariable=rsmtextEntryB)
tkgrid(rsmlabel1B, rsmtextEntryWidgetB)
OK.but72 <- tkbutton(rsm,text="Start", foreground = "red",command=function()rewrite_shared_mutations(tbn3, rsmtextEntryE5, rsmtextEntryE6, rsmtextEntryE7, rsmtextEntryA, rsmtextEntryB, txt))
tkgrid(OK.but72)
###set left:
tkgrid.configure(rsmlabel12, sticky="w")
tkgrid.configure(rsmlabel1E5, sticky="w")
tkgrid.configure(rsmlabel1E6, sticky="w")
tkgrid.configure(rsmlabel1E7, sticky="w")
tkgrid.configure(rsmlabel1A, sticky="w")
tkgrid.configure(rsmlabel1B, sticky="w")
tkgrid.configure(rsmlabel22, column=2, sticky="w")
tkgrid.configure(rsmtextEntryWidgetE5, column=2, sticky="w")
tkgrid.configure(rsmtextEntryWidgetE6, column=2, sticky="w")
tkgrid.configure(rsmtextEntryWidgetE7, column=2, sticky="w")
tkgrid.configure(rsmtextEntryWidgetA, column=2, sticky="w")
tkgrid.configure(rsmtextEntryWidgetB, column=2, sticky="w")
tkgrid.configure(button.widget_rsm2, column=3, sticky="e")
tkgrid.configure(OK.but72, column=3, sticky="e")
#--------------------------------------------------------HELP-TEXT-----------------------
txthelptbn <- tktext(helptbn,bg="white", font="Helvetica", width=20, wrap="word")
tkgrid(txthelptbn)
tkgrid.rowconfigure(txthelptbn,0,weight=1)
tkgrid.columnconfigure(txthelptbn,0,weight=1)
tkgrid.configure(txthelptbn,sticky='nswe')
helptbntext <- paste("##[Discover associations between point mutations and feature(s)]\n",
"\n",
"The input sequence alignment may consist either of DNA sequences (nucleotides) or amino acid sequences (amino acids). Undetermined nucleotides or amino acids have to be indicated by the letter 'X'.\n",
"\n",
"Sequences to analyze (FASTA)-MANDATORY: \n Sequence alignment file in FASTA format. Contains not only the sequences (as in usual FASTA files), but also feature information in the FASTA headers. See also tutorial.\n",
"\n",
"SeqFeatR can use either single features (ckeck 'One feature') or HLA-type like features. Single features are indicated in the FASTA headers as character strings (such as 'yes', 'no', '1', '2', '3', etc. - without the quotes) at the end of the FASTA headers, separated from the first part of the FASTA header by a semicolon. Alternatively, HLA-type-like features can be used in the FASTA headers, formatted in a block-structure. Here SeqFeatR has to be told where these blocks in the header are to be found.\n",
"\n",
"##[Visualize odds ratios and p-values]\n",
"\n",
"It is important to enter the correct columns. Please count them inside the csv result file from 'discover associations between point mutations and features'."
)
tryCatch({tkinsert(txthelptbn,"end",helptbntext)}, error = function(err) {})
tkconfigure(txthelptbn, state="disabled")
#-----
txthelptbn2 <- tktext(helptbn2,bg="white", font="Helvetica", width=20, wrap="word")
tkgrid(txthelptbn2)
tkgrid.rowconfigure(txthelptbn2,0,weight=1)
tkgrid.columnconfigure(txthelptbn2,0,weight=1)
tkgrid.configure(txthelptbn2,sticky='nswe')
helptbn2text <- paste("##[Discovering associations between mutation pairs and features]\n",
"\n",
"Find those position pairs above the chosen threshold which have an p-value above the chosen threshold.\n",
"You can choose whether to use feature specific analysis or not\n",
"\n",
"##[Discovering associations between mutation n-tuple and features]\n",
"\n",
"Find those position tuple(more than two members possible) which have an p-value above the chosen threshold from the analysis of point mutations and features."
)
tryCatch({tkinsert(txthelptbn2,"end",helptbn2text)}, error = function(err) {})
tkconfigure(txthelptbn2, state="disabled")
#-----
txthelptbn5 <- tktext(helptbn5,bg="white", font="Helvetica", width=20, wrap="word")
tkgrid(txthelptbn5)
tkgrid.rowconfigure(txthelptbn5,0,weight=1)
tkgrid.columnconfigure(txthelptbn5,0,weight=1)
tkgrid.configure(txthelptbn5,sticky='nswe')
helptbn5text <- paste("##[Tartan plot]\n",
"\n",
"For the tartan plot you can compare the results of two different pair mutation files. Be aware that for the additional ticks and notes in the plot you have to enter values which are inside the range of the sequence length which created this data.\n"
)
tryCatch({tkinsert(txthelptbn5,"end",helptbn5text)}, error = function(err) {})
tkconfigure(txthelptbn5, state="disabled")
#-----
txthelptbn3 <- tktext(helptbn3,bg="white", font="Helvetica", width=20, wrap="word")
tkgrid(txthelptbn3)
tkgrid.rowconfigure(txthelptbn3,0,weight=1)
tkgrid.columnconfigure(txthelptbn3,0,weight=1)
tkgrid.configure(txthelptbn3,sticky='nswe')
helptbn3text <- paste("##[Calculate q-values]\n",
"\n",
"The file for added q-value column has to have a column with \"p_value\" (not p-value!!) as heading.\n",
"\n",
"##[Founder effect finder]\n",
"\n",
"For analysis of a possible founder effect DON'T use a pair mutation result which differentiates between identifiers.\n"
)
tryCatch({tkinsert(txthelptbn3,"end",helptbn3text)}, error = function(err) {})
tkconfigure(txthelptbn3, state="disabled")
#--------------------------------------------------------TOOL-TIPS-----------------------
tk2tip(cb01, "If checked: FASTA file has to have nucleotides, if not amino acids.")
tk2tip(icb01, "If checked: data has only one feature (like tropism), if not two (like HLA types).")
tk2tip(button.widget_epi1, "Loads FASTA file with sequence alignment.")
tk2tip(button.widget_epi2, "Loads file with known epitopes. See example files.")
tk2tip(button.widget_epi3, "Loads file with known binding motifs. See example files.")
tk2tip(button.widget_epi4, "Load reference sequence for own position corrections, if you deleted position columns due to lots of gaps.")
tk2tip(textEntryWidgetC, "The minimum number of patients of one HLA type to consider in the calculation.")
tk2tip(textEntryWidgetD, "The optical level height of \"significant\" results in the graphical output.")
tk2tip(textEntryWidgetE, "The optical level height of \"star level\" results in the graphical output.")
tk2tip(OK.bute1, "Starts the calculation.")
tk2tip(textEntryWidgetH, "The position of the start of the first feature A allele in the description block of the FASTA file.")
tk2tip(textEntryWidgetH1, "The position of the end of the first feature A allele in the description block of the FASTA file.")
tk2tip(textEntryWidgetH2, "The position of the start of the second feature A allele in the description block of the FASTA file.")
tk2tip(textEntryWidgetH12,"The position of the end of the second feature A allele in the description block of the FASTA file.")
tk2tip(textEntryWidgetHB, "The position of the start of the first feature B allele in the description block of the FASTA file.")
tk2tip(textEntryWidgetH1B, "The position of the end of the first feature B allele in the description block of the FASTA file.")
tk2tip(textEntryWidgetH2B, "The position of the start of the second feature B allele in the description block of the FASTA file.")
tk2tip(textEntryWidgetH12B, "The position of the end of the second feature B allele in the description block of the FASTA file.")
tk2tip(cb0e, "Should a check for a phylogenetic bias be made?")
#tk2tip(textEntryWidgetKIB, "Which matrix should be applied for phylogenetic bias check?")
tk2tip(ddb, "Input can be: \"holm\", \"hochberg\", \"hommel\", \"bonferroni\", \"BH\", \"BY\", \"fdr\", \"none\" .")
tk2tip(textEntryWidgetH42B, "The size of the sliding window for graphical output. Must be greater than 1, ideally between 8-10 for class I HLA allels.")
tk2tip(Bbutton.widget_epi, "Loads csv file with results from 'Discover associations between point mutations and feature(s)'.")
tk2tip(BtextEntryWidgetA, "The separator used in the csv file.")
tk2tip(BtextEntryWidgetB, "The number of feature(s) in the csv file.")
tk2tip(BtextEntryWidgetC, "The first column with odds ratios.")
tk2tip(BtextEntryWidgetD, "The first column with p-values.")
tk2tip(BtextEntryWidgetE, "The column number with the name for the feature in the first row.")
tk2tip(BtextEntryWidgetF, "The number of columns for one identifier.")
tk2tip(BtextEntryWidgetG, "The first column of nucleotides/ amino acids (if existent).")
tk2tip(BtextEntryWidgetH, "The maximum value on the y-axis (minus and plus).")
tk2tip(BtextEntryWidgetI, "The main interval on the y-axis.")
tk2tip(BtextEntryWidgetJ, "If a color should be added, enter column number from csv file with values between 0 and 1.")
tk2tip(BtextEntryWidgetK, "Select with integer values if you want the first color further down.")
tk2tip(ddb2, "If p-values or OR should be plotted as height. P for p-value, OR for Odds ratios.")
tk2tip(BOK.bute2, "Starts the plot making.")
tk2tip(button.widget_epa1, "Loads FASTA file with sequences alignment.")
tk2tip(button.widget_epa2, "Loads file with results from 'Discover associations between point mutations and feature(s)'.")
tk2tip(button.widget_epa3, "Loads file with results from Tuple analysis.")
tk2tip(textEntry_Wp.value, "p-value for selecting results from Tuple analysis.")
tk2tip(OK.bute2, "Starts the calculation.")
#----
tk2tip(cb1, "Should analysis include different allels or compare to consensus?")
#----
tk2tip(cb, "Should analysis include different allels or compare to consensus?")
tk2tip(button.widget_co1, "Loads FASTA file with sequences alignment.")
tk2tip(button.widget_co2, "Loads file with consensus of sequences in FASTA file.")
tk2tip(cMtextEntryWidgetC, "The minimal number of patients which have the same feature type to be included in the analysis.")
tk2tip(cMtextEntryWidgetD, "p-value below which possible Tuple positions are included in the analysis.")
tk2tip(ddbc, "Input can be: \"holm\", \"hochberg\", \"hommel\", \"bonferroni\", \"BH\", \"BY\", \"fdr\", \"none\".")
tk2tip(cbm, "Should calculation be made with more than one core?")
tk2tip(OK.but21, "Starts the calculation.")
tk2tip(textEntryWidgetHC, "The position of the start of the first feature A allele in the description block of the FASTA file.")
tk2tip(textEntryWidgetH1C, "The position of the end of the first feature A allele in the description block of the FASTA file.")
tk2tip(textEntryWidgetH2C, "The position of the start of the second feature A allele in the description block of the FASTA file.")
tk2tip(textEntryWidgetH12C,"The position of the end of the second feature A allele in the description block of the FASTA file.")
tk2tip(textEntryWidgetHBC, "The position of the start of the first feature B allele in the description block of the FASTA file.")
tk2tip(textEntryWidgetH1BC, "The position of the end of the first feature B allele in the description block of the FASTA file.")
tk2tip(textEntryWidgetH2BC, "The position of the start of the second feature B allele in the description block of the FASTA file.")
tk2tip(textEntryWidgetH12BC, "The position of the end of the second feature B allele in the description block of the FASTA file.")
tk2tip(button.widget_com, "Loads Tuple results. Be careful with checking \"allels\" or \"no allels\".")
tk2tip(cMtextEntryWidgetE, "p-value for optical differentiation.")
tk2tip(OK.but22, "Starts the calculation.")
#----
tk2tip(Tbutton.widget_com, "The first file with two position columns and p-values (e.g. results from Tuple analysis).")
tk2tip(Tbutton.widget_com2, "The second file with two position columns and p-values (e.g. results from Tuple analysis).")
tk2tip(Tbutton.widget_com3, "A file with distance matrix values.")
tk2tip(TcMtextEntryWidgetE, "The optical space in pixle between the blocks.")
tk2tip(TcMtextEntryWidgetE1, "The colors of the plot, ranging from lowest to highest. Given as list: \"color1, color2, ...")
tk2tip(TcMtextEntryWidgetE2, "The positions for names for interesting positions. Given as list: \"pos1, pos2, ...\"")
tk2tip(TcMtextEntryWidgetE3, "The names for interesting positions. Given as list: \"name1, name2, ...\"")
tk2tip(TcMtextEntryWidgetE4, "The ticks on x and y axis.")
tk2tip(TcMtextEntryWidgetE5, "The column number of the first position in the first file.")
tk2tip(TcMtextEntryWidgetE6, "The column number of the second position in the first file.")
tk2tip(TcMtextEntryWidgetE7, "The column number of the value in the second file.")
tk2tip(TcMtextEntryWidgetE8, "The column number of the first position in the second file.")
tk2tip(TcMtextEntryWidgetE9, "The column number of the second position in the second file.")
tk2tip(TcMtextEntryWidgetE0, "The column number of the value in the first file.")
tk2tip(TOK.but22, "Starts the plotmaking")
#----
tk2tip(button.widget_sm1, "Loads FASTA file with sequences alignment.")
tk2tip(button.widget_sm2, "The result file from 'Discover associations between point mutations and feature(s)' or other file with positions and (p-)values.")
tk2tip(smtextEntryWidgetA, "The threshold below which a position should be taken for calculation.")
tk2tip(smtextEntryWidgetB, "The minimal number of tuple for position tuple.")
tk2tip(smtextEntryWidgetC, "The maximal number of tuple for position tuple.")
tk2tip(smtextEntryWidgetD, "The column number in which the feature is column name.")
tk2tip(smtextEntryWidgetE, "The column number of p-values for this feature.")
tk2tip(smtextEntryWidgetF, "The column number of amino acids/nucleotides for this feature.")
tk2tip(smtextEntryWidgetH, "The position of the start of the first feature A allele in the description block of the FASTA file.")
tk2tip(smtextEntryWidgetH1, "The position of the end of the first feature A allele in the description block of the FASTA file.")
tk2tip(smtextEntryWidgetH2, "The position of the start of the second feature A allele in the description block of the FASTA file.")
tk2tip(smtextEntryWidgetH12,"The position of the end of the second feature A allele in the description block of the FASTA file.")
tk2tip(smtextEntryWidgetHB, "The position of the start of the first feature B allele in the description block of the FASTA file.")
tk2tip(smtextEntryWidgetH1B, "The position of the end of the first feature B allele in the description block of the FASTA file.")
tk2tip(smtextEntryWidgetH2B, "The position of the start of the second feature B allele in the description block of the FASTA file.")
tk2tip(smtextEntryWidgetH12B, "The position of the end of the second feature B allele in the description block of the FASTA file.")
tk2tip(smtextEntryWidgetX , "The feature which should be analyzed (if there is a single one).")
tk2tip(OK.but4, "Starts the calculation.")
#----
tk2tip(button.widget_q, "Load file with \"p_value\" column.")
tk2tip(OK.but3, "Starts the calculation.")
tk2tip(button.widget_fe1, "Loads FASTA file with sequence alignment.")
tk2tip(button.widget_fe2, "Loads Tuple results. Not possible in combination with \"allels\".")
tk2tip(button.widget_fe3, "Loads tree file in nexus format.")
tk2tip(fetextEntryWidgetE, "Rate of co-mutation is in subtree vs is not in subtree.")
tk2tip(OK.but62, "Starts the calculation")
tk2tip(rsmtextEntryWidgetA, "The separator used in the csv file.")
tk2tip(rsmtextEntryWidgetB, "p-value for selecting intresting sequence positions.")
tk2tip(rsmtextEntryWidgetE5, "Column number with first sequence position.")
tk2tip(rsmtextEntryWidgetE6, "Column number with second sequence position.")
tk2tip(rsmtextEntryWidgetE7, "Column number with p-values.")
tk2tip(gFtextEntryWidgetC, "Starting position of the epitope in the alignment.")
tk2tip(gFtextEntryWidgetD, "Ending position of the epitope in the alignment.")
tk2tip(gFtextEntryWidgetF, "The minimum number of patients of one HLA type to consider in the calculation.")
tk2tip(gFtextEntryWidgetH, "The position of the start of the first feature A allele in the description block of the FASTA file.")
tk2tip(gFtextEntryWidgetH1, "The position of the end of the first feature A allele in the description block of the FASTA file.")
tk2tip(gFtextEntryWidgetH2, "The position of the start of the second feature A allele in the description block of the FASTA file.")
tk2tip(gFtextEntryWidgetH12, "The position of the end of the second feature A allele in the description block of the FASTA file.")
tk2tip(gFtextEntryWidgetHB, "The position of the start of the first feature B allele in the description block of the FASTA file.")
tk2tip(gFtextEntryWidgetH1B, "The position of the end of the first feature B allele in the description block of the FASTA file.")
tk2tip(gFtextEntryWidgetH2B, "The position of the start of the second feature B allele in the description block of the FASTA file.")
tk2tip(gFtextEntryWidgetH12B, "The position of the end of the second feature B allele in the description block of the FASTA file.")
tk2tip(sMAtextEntryWidgetC, "Feature for which the plot should be made.")
tk2tip(cb0sMA, "Should the corrected values be used?")
tk2tip(sMAtextEntryWidgetF, "The x-axis-breaks.")
#---------------------------------------------------------
tkbind(tt, "<Destroy>", function() tkdestroy(tn))
tkselect(tn, 0)
#-------------FOR CONFIG--------------------------------------------
z <- list()
z$cbValue01 <- list(cbValue01, "DNA")
z$cbValue_0e <- list(cbValue_0e, "Phylogenetic comparison")
z$cbValue_bayes_factor <- list(cbValue_bayes_factor, "Bayes Factor")
z$cbValue_K <- list(cbValue_K, "Constant Dirichlet precision parameter")
z$textEntryC <- list(textEntryC, "Number of patients threshold")
z$textEntryD <- list(textEntryD, "Height of horizontal bar")
z$textEntryE <- list(textEntryE, "Height of star level")
z$cbValue_0eG1 <- list(cbValue_0eG1, "pos_epi_plot")
z$cbValue_0eG1C <- list(cbValue_0eG1C, "has_C")
z$textEntryH <- list(textEntryH, "HLA-A1")
z$textEntryH1 <- list(textEntryH1, "HLA-A2")
z$textEntryH2 <- list(textEntryH2, "HLA-A3")
z$textEntryH12 <- list(textEntryH12, "HLA-A4")
z$textEntryHB <- list(textEntryHB, "HLA-B1")
z$textEntryH1B <- list(textEntryH1B, "HLA-B2")
z$textEntryH2B <- list(textEntryH2B, "HLA-B3")
z$textEntryH12B <- list(textEntryH12B, "HLA-B4")
z$textEntryHCC <- list(textEntryHCC, "HLA-C1")
z$textEntryH1CC <- list(textEntryH1CC, "HLA-C2")
z$textEntryH2CC <- list(textEntryH2CC, "HLA-C3")
z$textEntryH12CC <- list(textEntryH12CC, "HLA-C4")
z$textEntryIB <- list(textEntryIB, "p-value correction")
#z$textEntryKIB <- list(textEntryKIB, "Matrix for phylo")
z$dirichlet_precision_parameter_textEntry<- list(dirichlet_precision_parameter_textEntry, "Dirichlet precision parameter")
z$icbValue01 <- list(icbValue01, "One identifier")
z$textEntryH42B <- list(textEntryH42B, "window_size")
z$textEntry_p.value <- list(textEntry_p.value, "p-value addon")
z$BtextEntryA <- list(BtextEntryA, "csv seperator")
z$BtextEntryB <- list(BtextEntryB, "number of cases")
z$BtextEntryC <- list(BtextEntryC, "position of odds.ratio")
z$BtextEntryD <- list(BtextEntryD, "position of p.values")
z$BtextEntryE <- list(BtextEntryE, "name for the y-axis label")
z$BtextEntryF <- list(BtextEntryF, "frequency")
z$BtextEntryG <- list(BtextEntryG, "position of amino acid")
z$BtextEntryH <- list(BtextEntryH, "maximum value of y-axis")
z$BtextEntryI <- list(BtextEntryI, "intervall of y-axis")
z$BtextEntryJ <- list(BtextEntryJ, "add color information")
z$BtextEntryK <- list(BtextEntryK, "bias")
z$cMtextEntryC <- list(cMtextEntryC, "Number of patients threshold_cm")
z$cMtextEntryD <- list(cMtextEntryD, "level for significance")
z$cmtextEntryIB <- list(cmtextEntryIB, "cmp-value correction")
z$cbValuem <- list(cbValuem, "More than one core")
z$textEntryHC <- list(textEntryHC, "cmHLA-A1")
z$textEntryH1C <- list(textEntryH1C, "cmHLA-A2")
z$textEntryH2C <- list(textEntryH2C, "cmHLA-A3")
z$textEntryH12C <- list(textEntryH12C,"cmHLA-A4")
z$textEntryHBC <- list(textEntryHBC, "cmHLA-B1")
z$textEntryH1BC <- list(textEntryH1BC, "cmHLA-B2")
z$textEntryH2BC <- list(textEntryH2BC, "cmHLA-B3")
z$textEntryH12BC <- list(textEntryH12BC, "cmHLA-B4")
z$fetextEntryE <- list(fetextEntryE, "Ratio in subtree")
z$cMtextEntryE <- list(cMtextEntryE, "cMlevel for significance")
z$TcMtextEntryE <- list(TcMtextEntryE, "space between blocks")
z$TcMtextEntryE1 <- list(TcMtextEntryE1, "colors of the plot")
z$TcMtextEntryE2 <- list(TcMtextEntryE2, "name positions")
z$TcMtextEntryE3 <- list(TcMtextEntryE3, "names")
z$TcMtextEntryE4 <- list(TcMtextEntryE4, "ticks")
z$TcMtextEntryE5 <- list(TcMtextEntryE5, "column of first position in first file")
z$TcMtextEntryE6 <- list(TcMtextEntryE6, "column of second position in first file")
z$TcMtextEntryE7 <- list(TcMtextEntryE7, "column of values in first file")
z$TcMtextEntryE8 <- list(TcMtextEntryE8, "column of first position in second file")
z$TcMtextEntryE9 <- list(TcMtextEntryE9, "column of second position in second file")
z$TcMtextEntryE0 <- list(TcMtextEntryE0, "column of values in second file")
z$smtextEntryA <- list(smtextEntryA, "threshold")
z$smtextEntryB <- list(smtextEntryB, "min_number_of_ele_in_tupel")
z$smtextEntryC <- list(smtextEntryC, "max_number_of_ele_in_tupel")
z$cbValue_0sM <- list(cbValue_0sM, "column")
z$cbValue_0sM2 <- list(cbValue_0sM2, "column of position")
z$smtextEntryE <- list(smtextEntryE, "column of values")
z$smtextEntryF <- list(smtextEntryF, "column of aas")
z$smtextEntryH <- list(smtextEntryH, "smHLA-A1")
z$smtextEntryH1 <- list(smtextEntryH1, "smHLA-A2")
z$smtextEntryH2 <- list(smtextEntryH2, "smHLA-A3")
z$smtextEntryH12 <- list(smtextEntryH12,"smHLA-A4")
z$smtextEntryHB <- list(smtextEntryHB, "smHLA-B1")
z$smtextEntryH1B <- list(smtextEntryH1B, "smHLA-B2")
z$smtextEntryH2B <- list(smtextEntryH2B, "smHLA-B3")
z$smtextEntryH12B <- list(smtextEntryH12B, "smHLA-B4")
z$smtextEntryidet <- list(smtextEntryidet, "Identifier")
z$rsmtextEntryE5 <- list(rsmtextEntryE5, "rw column of first position")
z$rsmtextEntryE6 <- list(rsmtextEntryE6, "rw column of second position")
z$rsmtextEntryE7 <- list(rsmtextEntryE7, "rw column of values")
z$rsmtextEntryA <- list(rsmtextEntryA, "rw csv seperator")
z$rsmtextEntryB <- list(rsmtextEntryB, "rw threshold")
z$gFtextEntryC <- list(gFtextEntryC, "Epi start")
z$gFtextEntryD <- list(gFtextEntryD, "Epi end")
z$gFtextEntryF <- list(gFtextEntryF, "Number of patients threshold")
z$gFtextEntryH <- list(gFtextEntryH, "gFHLA-A1")
z$gFtextEntryH1 <- list(gFtextEntryH1, "gFHLA-A2")
z$gFtextEntryH2 <- list(gFtextEntryH2, "gFHLA-A3")
z$gFtextEntryH12 <- list(gFtextEntryH12, "gFHLA-A4")
z$gFtextEntryHB <- list(gFtextEntryHB, "gFHLA-B1")
z$gFtextEntryH1B <- list(gFtextEntryH1B, "gFHLA-B2")
z$gFtextEntryH2B <- list(gFtextEntryH2B, "gFHLA-B3")
z$gFtextEntryH12B <- list(gFtextEntryH12B, "gFHLA-B4")
z$sMAtextEntryC <- list(sMAtextEntryC, "Feat")
z$cbValue_0sMA <- list(cbValue_0sMA, "corrected")
z$sMAtextEntryF <- list(sMAtextEntryF, "axis_breaks")
.GlobalEnv[["z"]] <- z
#---------------------------------------------------------
},ex=function(){
SeqFeatR_GUI()
})
#SeqFeatR_GUI()
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