Nothing
R/hz.read.parameters.R
In cRacker: R-script suite for automated processing of proteomic peptide lists
hz.read.parameters <-
function( image.path = NULL,
build.matrix = "1",
.bg = "lightgrey",
path2,
path2.set,
.data,
path1
) {
##d9d9d9
#.bg = "red"
require(tcltk)
require(tcltk2)
print("test")
done <- tclVar(0)
print("starting GUI")
( path1.backup <- path1)
( path2.backup <- path2)
print("test")
print(getwd())
license.text <- paste( "Copyright (C) <2011> \n<Henrik Zauber; Max Planck Institute for Molecular Plant Physiology>\n
This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with this program. If not, see <http://www.gnu.org/licenses/>")
try( function.file <- read.csv(paste(path1,"/help-file.csv",sep = ""), stringsAsFactors = FALSE)
)
if(!exists("function.file")){
try( function.file <- read.csv(paste(path1,"/help-file.csv.gz",sep = ""), stringsAsFactors = FALSE)
)
}
if(!exists("function.file")){ function.file <- ""
}else{
print("Read function.file successfully.")
}
tk2font.set("TkDefaultFont",settings= "-family Tahoma -size 10 -weight normal")
#.bg.col <- "#efefef"
fontHeading <- tkfont.create(family = "Tahoma",size=10,weight="bold")
hz.path.set <- function(title.q){
fileDir<-tclvalue(tkchooseDirectory(title=title.q))
return(ReadAffy(celfile.path = fileDir))}
########################################################################################
### GUI START #############################################################################
########################################################################################
spacer <- " "
tt3 <- tktoplevel(bg = .bg)
tkwm.title(tt3,"cRacker")
tkwm.resizable(tt3, "FALSE","FALSE")
topMenu <- tk2menu(tt3,background = .bg)
tkconfigure(tt3,menu=topMenu,background = .bg)
fileMenu <- tk2menu(topMenu,tearoff=FALSE,background = .bg)
go.libraryMenu <- tk2menu(topMenu,tearoff=FALSE,background = .bg)
tt2 <- tkframe(tt3,bg = .bg)
if(is.null(image.path) == FALSE& 1==0){
.wd.image <- getwd()
setwd(image.path)
error.try <- class(try( .cra.img <- tkimage.create("photo", file=paste(path1,"/cRacker-logo-grey.pnm",sep = ""))))
if(error.try == "try-error"){.cra.img <- ""}
.cra <- tk2label(tt2,image = .cra.img,background = .bg)
setwd(.wd.image)
image.file <- TRUE
}else{image.file <- FALSE}
########
# loading:
#######
tk.loading <- tktoplevel(background = .bg)
tkfocus(tk.loading)
tkgrid(tklabel(tk.loading,text="Loading, please be patient",background = .bg))
if(image.file){
tkgrid(tklabel(tk.loading,image=.cra.img,background = .bg))
}
#load settings-files
if(path2.set$settings == "default" | !exists("path2.set")|exists(".data2")){
print("loaded settings")
try(load(paste(path1,"/settings.Rdata",sep = "")))
print("test")
}else{
print("loaded selected settings")
try(load(path2.set$settings))
}
#tkwm.geometry(tt2,"445x410+20+0")
if(!exists("settings")){
settings <- hz.cracker.default.settings()
}
info <- paste(license.text)
#tkgrid(image.button(tt2,"cRacker",info,image = .cra.img,fgcol = "white",bgcol = "white",size = 15,bf = "bold"),columnspan = 2,pady = 5)
label.width = 35
#####
# top down level
#####
# libraries
# GO
list.files.mapping <- list.files(paste((path1),sep = ""))
list.files.mapping <- list.files.mapping[grep("^cRackerMapping",list.files.mapping)]
tkadd( go.libraryMenu,
"command",
label="Add",
command=function(){
try(hz.go.input(path1))
tkmessageBox(title="Message",message="Finished Import\nPlease restart cRacker!",icon="warning",type="ok")
},background = .bg)
tkadd(go.libraryMenu,"command",label="Remove",
command=function(){hz.remove.data(type = "^cRackerMapping",path1 =tclvalue(path1))},background = .bg)
tkadd(fileMenu,"cascade",label="Mappings",menu=go.libraryMenu,background = .bg)
#emPAI
empai.libraryMenu <- tk2menu(topMenu,tearoff=FALSE)
tkadd( empai.libraryMenu,
"command",
label="Add",
command=function(){
try(hz.library.fasta(path1))
tkmessageBox(title="Message",message="Finished Import\nPlease restart cRacker!",icon="warning",type="ok")
})
tkadd(empai.libraryMenu,"command",label="Remove", command=function(){hz.remove.data(type = "^cRackerSequence|^cRackerEmPAI",path1 =tclvalue(path1))},background = .bg)
tkadd(fileMenu,"cascade",label="Protein Sequence library",menu=empai.libraryMenu,background = .bg)
tkadd(topMenu,"cascade",label="Libraries",menu=fileMenu,background = .bg)
######################
# choose quantitation type
######################
entryInit <- "ms-analysis"
entryWidth <- 20
question <- "Experiment Name"
tt2.var.expname <- tclVar(paste(entryInit))
textEntryWidget <- tkentry(tt2,width=paste(entryWidth),textvariable= tt2.var.expname)
if(image.file){image.input<- image.button(tt2,"cRacker",info,image = .cra.img,fgcol = "white",bgcol = "white",size = 3,bf = "bold")}else{
image.input <- help.button(tt2,"cRacker",buttontext = "cRacker")
}
tkgrid(tk2label(tt2,text=question,font = fontHeading,background = .bg,width = label.width),textEntryWidget, image.input,pady = 5,padx = 5)
tt2.experiment.name <- tclVar("1.x")
tkgrid(tk2separator(tt2),sticky = "we",columnspan = 3,pady = 5)
######
# Quantitation method
######
quant.method.button <- "switch to emPAI"
empai.button <- tk2button(tt2,text=quant.method.button ,command=function() {tkdestroy(tt3);path1 <- path1.backup;path2 <- path2.backup;tclvalue(done) <- 3})
tkgrid(tklabel(tt2,text= hz.function.file(function.file,"QM")[2] ,font = fontHeading,width = label.width ,background = .bg,justify = "center",compound = "center"),empai.button,help.button(tt2,hz.function.file(function.file,"QM")[2], hz.function.file(function.file,"QM")[3]))
tkgrid(tklabel(tt2,text=">> IonIntensities <<",fg = "red",bg = .bg),sticky = "s",columnspan = 3)
########################################################################################################################
### TAB
########################################################################################################################
tabs <- c(
tab1 <- "Main",
tab2 <- "Peptides -> Protein",
tab3 <- "Extra",
tab4 <- "Quantitation Mode",
tab5 <- "Statistics",
tab5.1 <- "Plotting",
tab6 <- "Paths"
)
nb <- tk2notebook(tt2, tabs = tabs) # starts notebook
# Make non selected tabs a little darker
#tcl("ttk::style", "configure", "TNotebook.Pane", forground = "blue",background="skyblue3")
#tcl("ttk::style", "map", "TNotebook.Tab", background=c("active", "skyblue"))
#tcl("ttk::style", "map", "TNotebook.Tab", background=c("active", "skyblue"))
#tcl("ttk::style", "configure", "TNotebook.Pane", forground=c("red"))
#tcl("ttk::style", "configure", "TNotebook.Pane", forground=c("red"))
tkgrid(nb,columnspan = 3,padx=5)
# first tab:
tb1 <- tk2notetab(nb, tab1)
tb2 <- tk2notetab(nb, tab2)
tb3 <- tk2notetab(nb, tab3)
tb4 <- tk2notetab(nb, tab4)
tb5 <- tk2notetab(nb, tab5)
tb5.1 <- tk2notetab(nb, tab5.1)
tb6 <- tk2notetab(nb, tab6)
pad.val <- 2
pad.y <- 2
tcl("ttk::style", "configure", "TNotebook", background=.bg)
tcl("ttk::style", "configure", "TNotebook.Tab",foreground = "black", background=.bg)
#tcl("ttk::style", "map", "TNotebook.Tab",foreground = c("focus", "red"))
tcl("ttk::style", "map", "TNotebook.Tab",foreground = c("active", "red"))
#tcl("ttk::style", "configure", "TNotebook", foreground = .bg,background=.bg)
#tcl("ttk::style", "configure", "TNotebook.Pane", background=.bg)
# Make non selected tabs a little darker
#tcl("ttk::style", "configure", "TNotebook.Pane", forground = "blue",background="skyblue3")
#tcl("ttk::style", "map", "TNotebook.Tab", background=c("active", "skyblue"))
#tcl("ttk::style", "map", "TNotebook.Tab", background=c("active", "skyblue"))
tcl("ttk::style", "configure", "TNotebook.Tab", foreground=c("black"))
tcl("ttk::style", "configure", "TNotebook.Pane", foreground=c("red"))
######
# Replicates
######
cb3 <- tk2checkbutton(tb1)
tb1.val.replicates <- tclVar(settings$tb1.val.replicates)
tkconfigure(cb3,variable=tb1.val.replicates)
tkgrid(tk2label(tb1,text= hz.function.file(function.file,"AR")[2],font = fontHeading,width = label.width ),cb3,help.button(tb1,hz.function.file(function.file,"AR")[2] ,hz.function.file(function.file,"AR")[3]),padx = pad.val, pady = pad.y,sticky = "we")
######
# common peptides:
######
help.tb1.replicate.cp <- "Only active if \"Replicates\" option is used. An additional normalization factor is created based on the mean relative change of common peptides between replicate samples."
cb4 <- tk2checkbutton(tb1)
tb1.val.replicates.cp <- tclVar(0)#settings$tb1.val.replicates.cp
tkconfigure(cb4,variable=tb1.val.replicates.cp)
#tkgrid(tk2label(tb1,text=title.t <- "normalise on common peptides",width = label.width),cb4,help.button(tb1,title.t ,help.tb1.replicate.cp),padx = pad.val, pady = pad.y,sticky = "we")
#tkgrid(tk2label(tb1,text=spacer, width = label.width ),padx = pad.val, pady = pad.y,columnspan = 3)
######
# merging Peptides
######
####
# protein.intensity
####
#tkgrid(tk2label(tb1,text=spacer,width = label.width ),columnspan = 3,padx = pad.val, pady = pad.y,sticky = "we")
tb1.var.protein.intensity <- c("mean","median","sum")
tb1.val.protein.intensity <- tclVar()
tclvalue(tb1.val.protein.intensity) <- settings$tb1.var.protein.intensity
comboBox <- ttkcombobox(tb1,values=tb1.var.protein.intensity,textvariable = tb1.val.protein.intensity,width = 17,state = "readonly")
tkgrid(tk2label(tb1,text = hz.function.file(function.file,"AM")[2],font = fontHeading,width = label.width ),comboBox,help.button(tb1,hz.function.file(function.file,"AM")[2], hz.function.file(function.file,"AM")[3]),padx = pad.val, pady = pad.y,sticky = "we")
####
# duplicate peptides
####
#tkgrid(tk2label(tb1,text=spacer,width = label.width ),columnspan = 3,padx = pad.val, pady = pad.y,sticky = "we")
tb1.duplicates.var <- c("mean","sum","max","min","exclude")
tb1.val.pep.duplicates <- tclVar()
tclvalue(tb1.val.pep.duplicates) <- settings$tb1.duplicates.var
comboBox <- ttkcombobox(tb1,values=tb1.duplicates.var,textvariable = tb1.val.pep.duplicates,width = 17,state = "readonly")
tkgrid(tk2label(tb1,text=hz.function.file(function.file,"PD")[2],font = fontHeading,width = label.width ),comboBox,help.button(tb1,hz.function.file(function.file,"PD")[2] , hz.function.file(function.file,"PD")[3]),padx = pad.val, pady = pad.y,sticky = "we")
######
# contaminants
######
cb4 <- tk2checkbutton(tb1)
tb1.val.conrev <- tclVar(settings$tb1.val.conrev)
tkconfigure(cb4,variable=tb1.val.conrev)
tkgrid(tk2label(tb1,text= hz.function.file(function.file,"ExCR")[2],font = fontHeading,width = label.width ),cb4,help.button(tb1,hz.function.file(function.file,"ExCR")[2] ,hz.function.file(function.file,"ExCR")[3]),padx = pad.val, pady = pad.y,sticky = "we")
#######
# tab 2
#######
pad.val <- pad.val
######
# score
######
entryWidth <- 40
tb2.val.score <- tclVar(settings$tb2.val.score)
textEntryWidget <- tkentry(tb2,width=paste(entryWidth),textvariable=tb2.val.score,width = 20)
tkgrid(tk2label(tb2,text=hz.function.file(function.file,"PST")[2],font = fontHeading,width = label.width ),textEntryWidget,help.button(tb2,hz.function.file(function.file,"PST")[2],hz.function.file(function.file,"PST")[3]),padx = pad.val, pady = pad.y,sticky = "we")
######
# Tab2
#####
####
# normalization
####
cb <- tk2checkbutton(tb2)
tb2.var.rownorm <- tclVar(settings$tb2.var.rownorm)
tkconfigure(cb,variable=tb2.var.rownorm)
tkgrid(tk2label(tb2,text=hz.function.file(function.file,"SaS")[2],font = fontHeading,width = label.width ),cb,help.button(tb2,hz.function.file(function.file,"SaS")[2] ,hz.function.file(function.file,"SaS")[3]),padx = pad.val, pady = pad.y,sticky = "we")
####
# norm.method
####
tb2.var.norm.method <- c("mean","median","z-score")
tb2.val.norm.method <- tclVar()
tclvalue(tb2.val.norm.method) <- settings$tb2.norm.method
comboBox <- ttkcombobox(tb2,values=tb2.var.norm.method,textvariable = tb2.val.norm.method,width = 17,state = "readonly")
tkgrid(tk2label(tb2,text=hz.function.file(function.file,"SM")[2],font = fontHeading,width = label.width ),comboBox,help.button(tb2,hz.function.file(function.file,"SM")[2] , hz.function.file(function.file,"SM")[3]),padx = pad.val, pady = pad.y,sticky = "nwe")
####
# shape
####
tb2.var.shape <- tclVar(settings$tb2.var.shape)
SliderValueLabel <- tk2label(tb2,text=tclvalue(tb2.var.shape))
tkconfigure(SliderValueLabel,textvariable= tb2.var.shape)
slider <- tkscale(tb2, from=0, to=100,
variable= tb2.var.shape,
orient="horizontal",
resolution = 1,
showvalue = T,
length = 136,
bg = .bg
)
tkgrid(tk2label(tb2,text=hz.function.file(function.file,"PoaN")[2],font = fontHeading,width = label.width ),slider,help.button(tb2,hz.function.file(function.file,"PoaN")[2] ,hz.function.file(function.file,"PoaN")[3]),padx = pad.val, pady = pad.y,sticky = "we")
#####
# redundant pep
#####
cb <- tk2checkbutton(tb2)
tb2.var.red.pep <- tclVar(settings$tb2.var.red.pep)
tkconfigure(cb,variable=tb2.var.red.pep)
tkgrid(tk2label(tb2,text=hz.function.file(function.file,"EoRP")[2] ,font = fontHeading,width = label.width),cb,help.button(tb2,hz.function.file(function.file,"EoRP")[2] ,hz.function.file(function.file,"EoRP")[3]),sticky = "s",padx = pad.val, pady = pad.y,sticky = "we")
tb2.var.db <- tclVar()
tclvalue(tb2.var.db) <- settings$tb2.var.db
list.files.data <- list.files(paste(path1,sep = ""))
list.files.data <- list.files.data[grep("cRackerSequence-",list.files.data,fixed = T)]
list.files.data <- substring(list.files.data,17,nchar(list.files.data))
db <- as.character(list.files.data)
comboBox <- ttkcombobox(tb2,values=db,textvariable = tb2.var.db,width = 17,state = "readonly")
tkgrid(tk2label(tb2,text="search duplicates for exclusion"),comboBox,padx = pad.val, pady = pad.y,sticky = "we")
cbmq <- tk2checkbutton(tb2)
tb2.var.red.pep.mq <- tclVar(settings$tb2.var.red.pep.mq)
tkconfigure(cbmq,variable=tb2.var.red.pep.mq)
tkgrid(tk2label(tb2,text="use list info for exclusion" ),cbmq,sticky = "we")
# tab3
######
####
# PHospho
####
# tb4.4 <- tk2checkbutton(tb3)#
# tb3.var.phospho <- tclVar(settings$tb3.var.phospho)
#tkconfigure(tb4.4,variable=tb3.var.phospho)
#tkgrid(tk2label(tb3,text=hz.function.file(function.file,"PP")[2],font = fontHeading,width = label.width ),tb4.4,help.button(tb3,hz.function.file(function.file,"PP")[2] ,hz.function.file(function.file,"PP")[3]),padx = pad.val, pady = pad.y,sticky = "we")
tb3.phospho <- c("none","peptide based analysis","protein based analysis")
tb3.var.phospho <- tclVar()
tclvalue(tb3.var.phospho) <- settings$tb3.phospho
comboBox <- ttkcombobox(tb3,values=tb3.phospho,textvariable = tb3.var.phospho,width = 17,state = "readonly")
tkgrid(tk2label(tb3,text=hz.function.file(function.file,"PP")[2],font = fontHeading,width = label.width ),comboBox,help.button(tb3,hz.function.file(function.file,"PP")[2] , hz.function.file(function.file,"PP")[3]),padx = pad.val, pady = pad.y,sticky = "we")
######
# outlier
######
#tkgrid(tk2label(tb3,text=spacer,width = label.width ),columnspan = 3,padx = pad.val, pady = pad.y,sticky = "we")
tb3.outlier <- c("none","outside both whiskers","outside lower whisker","top 3")
tb3.var.outlier <- tclVar()
tclvalue(tb3.var.outlier) <- settings$tb3.outlier
comboBox <- ttkcombobox(tb3,values=tb3.outlier,textvariable = tb3.var.outlier,width = 17,state = "readonly")
tkgrid(tk2label(tb3,text=hz.function.file(function.file,"OE")[2],font = fontHeading,width = label.width ),comboBox,help.button(tb3,hz.function.file(function.file,"OE")[2] , hz.function.file(function.file,"OE")[3]),padx = pad.val, pady = pad.y,sticky = "we")
######
# zero handling
######
entryWidth <- 5
tb3.val.zero.treat <- tclVar(paste(settings$tb3.val.zero.treat ))
onArgEdit <- function () {
if (is.integer(tb3.val.zero.treat) == FALSE){
tclvalue(tb3.val.zero.treat) <- tclvalue(tb3.val.zero.treat)
tkconfigure(textEntryWidget, textvarible= tb3.val.zero.treat)
}
return(tclVar(is.integer(tb3.val.zero.treat))) # Must return TRUE to accept edition!
}
textEntryWidget <- tkentry(tb3,width=paste(entryWidth),textvariable= tb3.val.zero.treat,width = 19,validate = "none",validatecommand = onArgEdit)
tkgrid(tk2label(tb3,text=hz.function.file(function.file,"ZH")[2],font = fontHeading,width = label.width),textEntryWidget,help.button(tb3,hz.function.file(function.file,"ZH")[2], hz.function.file(function.file,"ZH")[3]),padx = pad.val, pady = pad.y,sticky = "we" )
####
# TAB4
pad.val = pad.val
pad.y = 0.5
######
# raw values
######
tb4.rb1 <- tk2radiobutton(tb4)
tb4.rb2 <- tk2radiobutton(tb4)
tb4.rb3 <- tk2radiobutton(tb4)
tb4.rb4 <- tk2radiobutton(tb4)
tb4.quant.method <- tclVar(settings$tb4.quant.method)
tkconfigure(tb4.rb1,variable=tb4.quant.method,value="lf")
tkconfigure(tb4.rb2,variable=tb4.quant.method,value="cbn")
tkconfigure(tb4.rb3,variable=tb4.quant.method,value="15n")
entryWidth <- 17
help.tb4.raw.values <-
tb4.val.raws <- c( "fraction of total (fot)",
"fot plus n correction (fotn)",#"fot 50", #"fotn 50",
"no normalization","equal.peptides")
tb4.val.raw.values <- tclVar()
tclvalue(tb4.val.raw.values ) <- settings$tb4.val.raw.values
if(length(grep(settings$tb4.val.raw.values,tb4.val.raws,fixed = TRUE))==0){tclvalue(tb4.val.raw.values ) <- tb4.val.raws[1]}
comboBox <- ttkcombobox(tb4,values=tb4.val.raws ,textvariable = tb4.val.raw.values, width = entryWidth ,state = "readonly")
tkgrid(tk2label(tb4,text=hz.function.file(function.file,"LF")[2],font = fontHeading,width = label.width),tb4.rb1,help.button(tb4,hz.function.file(function.file,"LF")[2], hz.function.file(function.file,"LF")[3]),padx = pad.val, pady = pad.y,sticky = "we")
tkgrid(tk2label(tb4,text = ""),comboBox,tk2label(tb4,text = ""))
#####
# CBN
#####
tb4.p <- tk2checkbutton(tb4)
tb4.var.cbn <- tclVar(settings$tb4.var.cbn)
tkconfigure(tb4.p,variable= tb4.var.cbn)
tkgrid(tk2label(tb4,text=hz.function.file(function.file,"RPN")[2],font = fontHeading,width = label.width),tb4.rb2,help.button(tb4,hz.function.file(function.file,"RPN")[2],hz.function.file(function.file,"RPN")[3]),padx = pad.val, pady = pad.y ,columnspan = 1,sticky = "we")
tb4.help1.1 <- "Choose if factor is used on raw data, or on scaled peptide data."
tb4.p2 <- tk2checkbutton(tb4)
tb4.var2.cbn <- tclVar(settings$tb4.var2.cbn)
tkconfigure(tb4.p2,variable= tb4.var2.cbn)
#tkgrid(tk2label(tb4,text="use on scaled peptides"),tb4.p2,help.button(tb4,"row norm",tb4.help1.1),padx = pad.val, pady = pad.y,sticky = "we")
question <- "Protein:"
tb4.help2.cbn <- "Define the Accession code of your reference Protein. Default is BSA."
tb4.val.cbn.prot <- tclVar(paste(settings$tb4.val.cbn.prot))
tb4.textEntryWidget <- tkentry(tb4,width=paste(entryWidth+3),textvariable=tb4.val.cbn.prot)
tkgrid(tk2label(tb4,text=hz.function.file(function.file,"RP")[2]),tb4.textEntryWidget,help.button(tb4,hz.function.file(function.file,"RP")[2],hz.function.file(function.file,"RP")[3]),padx = pad.val, pady = pad.y,sticky = "we")
####
# norm.prot shape
####
tb4.val.cbn.shape <- tclVar(settings$tb4.val.cbn.shape)
SliderValueLabel.tb4 <- tk2label(tb4,text=as.character(tclvalue(tb4.val.cbn.shape)))
tkconfigure(SliderValueLabel.tb4,textvariable=tb4.val.cbn.shape)
slider.tb4 <- tkscale(tb4, from=0, to=100,
variable=tb4.val.cbn.shape,
orient="horizontal",
resolution = 1,
showvalue = T
, length =paste(entryWidth+120),
bg = .bg)
tkgrid(tk2label(tb4,text = hz.function.file(function.file,"RPNS")[2] ),slider.tb4,help.button(tb4,hz.function.file(function.file,"RPNS")[2] ,hz.function.file(function.file,"RPNS")[3] ))
#tkgrid(tk2label(tb4,text=spacer),columnspan = 3)
#######
# tb4.val.n15
######
tb4.tb4.val.n15.p <- tk2checkbutton(tb4)
tb4.val.n15 <- tclVar(settings$tb4.val.n15)
tkconfigure(tb4.tb4.val.n15.p,variable= tb4.val.n15)
tkgrid(tk2label(tb4,text=hz.function.file(function.file,"LN")[2] ,font = fontHeading,width = label.width ),tb4.rb3,help.button(tb4,hz.function.file(function.file,"LN")[2] ,hz.function.file(function.file,"LN")[3] ),padx = pad.val, pady = pad.y,sticky = "we")
#####
# log
#####
tb4.tb4.val.n15.log.p <- tk2checkbutton(tb4)
tb4.val.n15.log <- tclVar(settings$tb4.val.n15.log)
tkconfigure(tb4.tb4.val.n15.log.p,variable= tb4.val.n15.log)
tkgrid(tk2label(tb4,text=hz.function.file(function.file,"LOG")[2] ),tb4.tb4.val.n15.log.p,help.button(tb4,hz.function.file(function.file,"LOG")[2],hz.function.file(function.file,"LOG")[3]),padx = pad.val, pady = pad.y,sticky = "we")
####
# n15.log.correction
####
tb4.var.n15.log.correction <- c("none","mean","median")
tb4.val.n15.log.correction <- tclVar()
tclvalue(tb4.val.n15.log.correction) <- settings$tb4.var.n15.log.correction
comboBox <- ttkcombobox(tb4,values=tb4.var.n15.log.correction,textvariable = tb4.val.n15.log.correction,width = 17,state = "readonly")
tkgrid(tk2label(tb4,text=hz.function.file(function.file,"CorLOG")[2]),comboBox,help.button(tb4,hz.function.file(function.file,"CorLOG")[2] , hz.function.file(function.file,"CorLOG")[3]),padx = pad.val, pady = pad.y,sticky = "we")
######
# ratio
######
######
entryWidth <- 5
tb4.val.ratio <- tclVar(paste(settings$tb4.val.ratio ))
onArgEdit <- function () {
if (is.integer(tb4.val.ratio) == FALSE){
tclvalue(tb4.val.ratio) <- settings$tb4.val.ratio
tkconfigure(textEntryWidget, textvariable= tb4.val.ratio)
}
return(tclVar(is.integer(tb4.val.ratio))) # Must return TRUE to accept edition!
}
textEntryWidget <- tkentry(tb4,width=paste(entryWidth),textvariable= tb4.val.ratio,width = 19,validate = "none",validatecommand = onArgEdit)
tkgrid(tk2label(tb4,text=hz.function.file(function.file,"ERLU")[2]),textEntryWidget,help.button(tb4,hz.function.file(function.file,"ERLU")[2], hz.function.file(function.file,"ERLU")[3]),padx = pad.val, pady = pad.y,sticky = "we" )
#tb5.1 <- tk2notebook(tb5, tabs = nb.tb5.names<- c("settings","plots")) # starts notebook
#tb5 <- tk2notetab(tb5.1, nb.tb5.names[1] )
#tb5.1.2 <- tk2notetab(tb5.1, nb.tb5.names[2] )
#tkgrid(tb5.1)
####
# cluster.method
####
tkframe.kmeans <- tk2frame(tb5 )
entryWidth <- 5
tb5.val.kmeans <- tclVar(paste(settings$tb5.val.kmeans ))
onArgEdit <- function () {
if (is.integer(tb5.val.kmeans) == FALSE){
tclvalue(tb5.val.kmeans) <- settings$tb5.val.kmeans
tkconfigure(textEntryWidget, textvariable= tb5.val.kmeans)
}
return(tclVar(is.integer(tb5.val.kmeans))) # Must return TRUE to accept edition!
}
textEntryWidget <- tkentry(tb5,width=paste(entryWidth),textvariable= tb5.val.kmeans,width = 5,validate = "none",validatecommand = onArgEdit)
tb5.var.cluster.method <- c("k-Means","hclust")
tb5.val.cluster.method <- tclVar()
tclvalue(tb5.val.cluster.method) <- settings$tb5.val.cluster.method
comboBox <- ttkcombobox(tkframe.kmeans,values=tb5.var.cluster.method,textvariable = tb5.val.cluster.method,width = 8,state = "readonly")
tkgrid(tk2label(tkframe.kmeans,text = "Clustering ",font = fontHeading,),comboBox,tk2label(tkframe.kmeans,text = " , cluster:"),columnspan = 3)
tkgrid(tkframe.kmeans, textEntryWidget,help.button(tb5,hz.function.file(function.file,"MTC")[2], hz.function.file(function.file,"MTC")[3]),padx = pad.val, pady = pad.y,sticky = "we")
#stop()
#tkgrid(tk2label(tb5,text=hz.function.file(function.file,"MTC")[2]),comboBox,help.button(tb5,hz.function.file(function.file,"MTC")[2], hz.function.file(function.file,"MTC")[3]),padx = pad.val, pady = pad.y,sticky = "we")
######
# anova.p
######
tkframe.anova.log2 <- tk2frame(tb5 )
anova.log.cb <- tk2checkbutton(tkframe.anova.log2)
tb5.val.anova.log2 <- tclVar(settings$tb5.val.anova.log2)
tkconfigure(anova.log.cb,variable=tb5.val.anova.log2)
entryWidth <- 5
tb5.val.anova.p <- tclVar(paste(settings$tb5.val.anova.p))
onArgEdit <- function () {
if (is.integer(tb5.val.anova.p) == FALSE){
tclvalue(tb5.val.anova.p) <- settings$tb5.val.anova.p
tkconfigure(textEntryWidget, textvariable= tb5.val.anova.p)
}
return(tclVar(is.integer(tb5.val.anova.p))) # Must return TRUE to accept edition!
}
textEntryWidget <- tkentry(tb5,width=paste(entryWidth),textvariable= tb5.val.anova.p,width = 19,validate = "none",validatecommand = onArgEdit)
tkgrid(tk2label(tkframe.anova.log2,text = paste(hz.function.file(function.file,"PANOVA")[2],"(log2"),font = fontHeading),anova.log.cb,tk2label(tkframe.anova.log2,text = "):",font= fontHeading),columnspan = 3,sticky = "we" )
tkgrid(tkframe.anova.log2,textEntryWidget,help.button(tb5,hz.function.file(function.file,"PANOVA")[2],hz.function.file(function.file,"PANOVA")[3]),padx = pad.val, pady = pad.y,sticky = "we" )
####
# p.adjust
####
tb5.var.p.adjust <- c("holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none")
tb5.val.p.adjust <- tclVar()
tclvalue(tb5.val.p.adjust) <- settings$tb5.var.p.adjust
comboBox <- ttkcombobox(tb5,values=tb5.var.p.adjust,textvariable = tb5.val.p.adjust,width = 17,state = "readonly")
tkgrid(tk2label(tb5,text=hz.function.file(function.file,"MTC")[2]),comboBox,help.button(tb5,hz.function.file(function.file,"MTC")[2], hz.function.file(function.file,"MTC")[3]),padx = pad.val, pady = pad.y,sticky = "we")
######
# onetailed
######
cb3 <- tk2checkbutton(tb5)
tb5.val.onetailed.ttest <- tclVar(settings$val.onetailed.ttest)
tkconfigure(cb3,variable=tb5.val.onetailed.ttest)
tkgrid(tk2label(tb5,text="Include one tailed t-test",width = label.width ),cb3,help.button(tb5,"Include one tailed t-test" ,""),padx = pad.val, pady = pad.y,sticky = "we")
####
# do.go
####
tb5.do.go.m <- tk2checkbutton(tb5)
tb5.var.do.go <- tclVar(settings$tb5.var.do.go)
tkconfigure(tb5.do.go.m,variable=tb5.var.do.go)
#tkgrid(tk2label(tb5,text=hz.function.file(function.file,"MAP")[2],font = fontHeading,width = label.width ),tb5.do.go.m,help.button(tb5,hz.function.file(function.file,"MAP")[2],hz.function.file(function.file,"MAP")[3]),padx = pad.val, pady = pad.y,sticky = "we")
####
# path Goterm
####
path1 <- tclVar(path1)
tb5.var.go.term.list <-c("none",as.character(gsub("^cRackerMapping-","",list.files.mapping)))
tb5.val.go.term.list <- tclVar()
tclvalue(tb5.val.go.term.list) <- settings$tb5.go.term.list
comboBox <- ttkcombobox(tb5,values=tb5.var.go.term.list,textvariable = tb5.val.go.term.list,width = 17,state = "readonly")
tkgrid(tk2label(tb5,text=hz.function.file(function.file,"MAPL")[2],font = fontHeading,width = label.width ),comboBox,help.button(tb5,hz.function.file(function.file,"MAPL")[2], hz.function.file(function.file,"MAPL")[3]),padx = pad.val, pady = pad.y,sticky = "we")
####
# Correlation Matrix
####
tb5.do.cor.help <-
"Choose the type of correlation for creating a cross correlation list."
#tkgrid(tk2label(tb5,text=spacer,width = label.width ),columnspan = 3,padx = pad.val, pady = pad.y,sticky = "we")
tb5.do.cor <- c("pearson", "kendall", "spearman","none")
tb5.val.do.cor <- tclVar()
tclvalue(tb5.val.do.cor) <- settings$tb5.do.cor
comboBox <- ttkcombobox(tb5,values=tb5.do.cor,textvariable = tb5.val.do.cor,width = 17,state = "readonly")
tkgrid(tk2label(tb5,text=hz.function.file(function.file,"CA")[2],font = fontHeading,width = label.width ),comboBox,help.button(tb5,hz.function.file(function.file,"CA")[2], hz.function.file(function.file,"CA")[3]),padx = pad.val, pady = pad.y,sticky = "we")
############
# network
############
do.network <- 0
tb5.do.network.m <- tk2checkbutton(tb5)
tb5.var.do.network <- tclVar(0)#tclVar(settings$tb5.var.do.network)
tkconfigure(tb5.do.network.m,variable=tb5.var.do.network)
#tkgrid(tk2label(tb5,text=hz.function.file(function.file,"PN")[2]),tb5.do.network.m,help.button(tb5,hz.function.file(function.file,"PN")[2],hz.function.file(function.file,"PN")[3]),padx = pad.val, pady = pad.y,sticky = "we")
######
# volcano
######
cb3 <- tk2checkbutton(tb5)
tb5.val.volcano <- tclVar(settings$tb5.val.volcano)
tkconfigure(cb3,variable=tb5.val.volcano)
tkgrid(tk2label(tb5,text=hz.function.file(function.file,"VP")[2],font = fontHeading,width = label.width ),cb3,help.button(tb5,hz.function.file(function.file,"VP")[2] ,hz.function.file(function.file,"VP")[3]),padx = pad.val, pady = pad.y,sticky = "we")
##########
# log2 ratio threshold
#########
tb5.var.log2.ratio.thres <- tclVar(settings$tb5.var.log2.ratio.thres)
SliderValueLabel <- tk2label(tb5,text=tclvalue(tb5.var.log2.ratio.thres))
tkconfigure(SliderValueLabel,textvariable= tb5.var.log2.ratio.thres)
slider <- tkscale( tb5, from=0, to=5,
variable= tb5.var.log2.ratio.thres,
orient="horizontal",
resolution = 0.1,
showvalue = T,
length = 136,
bg = .bg
)
tkgrid(tk2label(tb5,text=hz.function.file(function.file,"LRT")[2]),slider,help.button(tb5,hz.function.file(function.file,"LRT")[2] ,hz.function.file(function.file,"LRT")[3]),padx = pad.val, pady = pad.y,sticky = "we")
##########################################################################
########## tb5.1.2.fl.bp <- tk2labelframe(tb5.1.2) statistics
###########################################################################
label.width.temp <- 22
pad.y <- 2
pad.val <- 2
tb5.1.2.fl.bp <- tk2labelframe(tb5.1,text = "type of single protein plots")
tb5.1.2.fl.bp.frame <- tk2frame(tb5.1.2.fl.bp )
#############
parent.placeholder <- tb5.1.2.fl.bp.frame
tb5.1.2.fl.bp.frame.plot.type.var <- c("barplot","grouped barplot (based on time column)","lineplot","time series (all in one)","time series (single plot)")
tb5.nb.2.fl.bp.frame.val.plot.type <- tclVar()
tclvalue(tb5.nb.2.fl.bp.frame.val.plot.type) <- settings$tb5.nb.2.fl.bp.frame.val.plot.type
comboBox <- ttkcombobox(parent.placeholder,values=tb5.1.2.fl.bp.frame.plot.type.var,textvariable = tb5.nb.2.fl.bp.frame.val.plot.type,width = .width.temp<- 30,state = "readonly")
print("test")
tkgrid(tk2label(parent.placeholder,text=hz.function.file(function.file,"SPPT")[2],font = fontHeading,width = label.width.temp ),comboBox,help.button(parent.placeholder,hz.function.file(function.file,"SPPT")[2] , hz.function.file(function.file,"SPPT")[3]),padx = pad.val, pady = pad.y,sticky = "wen")
##############
tb5.1.2.fl.bp.frame.var.xlab <- tclVar(settings$tb5.nb.2.fl.bp.frame.var.xlab)
textEntryWidget <- tk2entry(parent.placeholder,width=.width.temp,textvariable= tb5.1.2.fl.bp.frame.var.xlab)
tkgrid(tk2label(parent.placeholder,text=hz.function.file(function.file,"XL")[2],font = fontHeading,width = label.width.temp),textEntryWidget, help.button(parent.placeholder,hz.function.file(function.file,"XL")[2] , hz.function.file(function.file,"XL")[3]),padx = pad.val, pady = pad.y,sticky = "wen")
##############
#############
tkgrid(tb5.1.2.fl.bp.frame,sticky = "wen",padx = pad.val, pady = pad.y,sticky = "we")
tkgrid(tb5.1.2.fl.bp,columnspan = 3, sticky = "wen",padx = pad.val, pady = pad.y,sticky = "we")
########
########
##########################################################################################
############
# color plots
############
#settings$tb5.color.plots <- "rainbow"
tb5.help.color.plots <- "Select the color mode for plot output."
#tkgrid(tk2label(tb5,text=spacer,width = label.width ),columnspan = 3,padx = pad.val, pady = pad.y,sticky = "we")
tb5.color.plots <- c("rainbow","colorblind","greytone")
tb5.var.color.plots <- tclVar()
tclvalue(tb5.var.color.plots) <- settings$tb5.var.color.plots
comboBox <- ttkcombobox(tb5.1,values=tb5.color.plots,textvariable = tb5.var.color.plots,width = 17,state = "readonly")
tkgrid(tk2label(tb5.1,text=hz.function.file(function.file,"CM")[2],font = fontHeading,width = label.width ),comboBox,help.button(tb5.1,hz.function.file(function.file,"CM")[2], hz.function.file(function.file,"CM")[3]),padx = pad.val, pady = pad.y,sticky = "we")
############
# graphic.type
############
#settings$tb5.graphic.type <- "rainbow"
tb5.help.graphic.type <- "Graphic type defines the graphic type, that is used for graphic output."
print("test")
#tkgrid(tk2label(tb5,text=spacer,width = label.width ),columnspan = 3,padx = pad.val, pady = pad.y,sticky = "we")
tb5.graphic.type <- c("pdf","eps")
tb5.var.graphic.type <- tclVar()
tclvalue(tb5.var.graphic.type) <- settings$tb5.var.graphic.type
comboBox <- ttkcombobox(tb5.1,values=tb5.graphic.type,textvariable = tb5.var.graphic.type,width = 17,state = "readonly")
tkgrid(tk2label(tb5.1,text=hz.function.file(function.file,"GT")[2],font = fontHeading,width = label.width ),comboBox,help.button(tb5.1,hz.function.file(function.file,"GT")[2], hz.function.file(function.file,"GT")[3]),padx = pad.val, pady = pad.y,sticky = "we")
####
# only plotting
####
plot.only <- FALSE
locationFrame <- tk2frame(tb5.1)
path5 <- tclVar("")
buttonRcmdr <- function(..., borderwidth, fg, foreground, relief) ttkbutton(...)
onBrowse <- function(){
tclvalue(path5) <- tclvalue(tkgetOpenFile(filetypes = "{{Rdata} {.Rdata}} {{All files} *}", initialdir = tclvalue(path2),parent = tt2))
}
browseButton <- buttonRcmdr(tb5.1, text=gettext("Browse", domain="R-Rcmdr"), width= 6, command=onBrowse, borderwidth=3)
locationField <- ttkentry(tb5.1, width=entryWidth, textvariable=path5)
locationScroll <- ttkscrollbar(tb5.1, orient="horizontal",
command=function(...) tkxview(tb5.1, ...))
tkconfigure(locationField, xscrollcommand=function(...) tkset(locationScroll, ...))
tkgrid(tk2label(tb5.1,text= hz.function.file(function.file,"SfR")[2],font = fontHeading,width = label.width ),locationField, browseButton,sticky = "we",padx = pad.val,pady = pad.y,sticky = "we")
######
# tab6
######
pad.val = 1
tkgrid(tk2label(tb6,text="Paths",font = fontHeading),sticky="w",padx = pad.val, pady = pad.y,sticky = "we")
#tkgrid(tk2label(tb6,text="selected folders:"),sticky="w",padx = pad.val, pady = pad.y,sticky = "we")
#path1 <- tclVar(path1)
path2 <- tclVar(path2)
path3 <- tclVar(paste(as.character(tclvalue(path1)),"scripts/script.shape.R",sep = ""))
buttonRcmdr <- function(..., borderwidth, fg, foreground, relief) ttkbutton(...)
entryWidth <- 37
question1 <- "Browse:"
question2 <- "data:"
question3 <- "Browse"
question4 <- "Browse"
path.width <- 16
locationFrame <- tk2labelframe(tb6,text = "cRacker path")
path1 <- path1
directoryFrame <- tk2frame(locationFrame)
onBrowse <- function(){
tclvalue(path1) <- tclvalue(tkchooseDirectory(initialdir = tclvalue(path1),parent = tt2))
}
browseButton <- buttonRcmdr(directoryFrame, text=gettext(question1, domain="R-Rcmdr"), width= path.width, command=onBrowse, borderwidth=3)
locationField <- ttkentry(directoryFrame, width=entryWidth, textvariable=path1)
test<- function(){tclvalue(path1) <- tclvalue(path1) }
test()
locationScroll <- ttkscrollbar(directoryFrame, orient="horizontal",
command=function(...) tkxview(locationField, ...))
tkconfigure(locationField, xscrollcommand=function(...) tkset(locationScroll, ...))
#tkgrid(browseButton,locationField, sticky="w",padx = pad.val, pady = pad.y,sticky = "we")
#tkgrid(directoryFrame, sticky="nw",padx = pad.val, pady = pad.y,sticky = "we")
#tkgrid(locationFrame, sticky="w",columnspan = 3,padx = pad.val, pady = pad.y,sticky = "we")
onBrowse <- function(){
tclvalue(path2) <- tclvalue(tkchooseDirectory(initialdir = tclvalue(path2),parent = tt2))
}
browseButton <- buttonRcmdr(directoryFrame, text=gettext(question2, domain="R-Rcmdr"), width=path.width, command=onBrowse, borderwidth=3)
locationField <- ttkentry(directoryFrame, width= entryWidth, textvariable=path2)
test<- function(){tclvalue(path2) <- tclvalue(path2) }
test()
locationScroll <- ttkscrollbar(directoryFrame, orient="horizontal",
command=function(...) tkxview(locationField, ...))
tkconfigure(locationField, xscrollcommand=function(...) tkset(locationScroll, ...))
#tkgrid(browseButton,locationField, sticky="w",padx = pad.val, pady = pad.y,sticky = "we")
#tkgrid(directoryFrame, sticky="nw",padx = pad.val, pady = pad.y,sticky = "we")
#tkgrid(locationFrame, sticky="we",padx = pad.val, pady = pad.y,sticky = "we")
####
#checkmark for personal shaping
###
#tkgrid(tk2label(tb6,text=" "),sticky="w",columnspan = 1,padx = pad.val, pady = pad.y,sticky = "we")
#locationFrame <- tk2labelframe(tb6)
#directoryFrame <- tk2frame(locationFrame)
path.labelframe <- tk2labelframe(tb6,text = "cRacker path")
path.frame <- tk2frame(path.labelframe)
path1.input <- tclvalue(path1)
path2.input <- tclvalue(path2)
tkgrid(tk2label(path.frame,text = "cracker:"),tk2label(tb6,text = hz.brake.strings(path1.input,70)),sticky = "wn")
tkgrid(tk2label(path.frame,text = "data path:"),tk2label(tb6,text = hz.brake.strings(path2.input,70)),sticky = "wn")
tkgrid(path.frame)
tkgrid(path.labelframe,sticky="ew",columnspan = 3)
#tkgrid(tk2label(tb6,text = "data path:"),tk2label(tb6,text = tclvalue(path2)))
tkgrid(tk2label(tb6,text="Advanced",font = fontHeading),sticky="w",padx = pad.val, pady = pad.y,sticky = "we")
#tkgrid(tk2label(directoryFrame,text="personal shape"),tb6.p,help.button(tb6,"Labeling",tb6.help.shape.script),sticky = "w",columnspan = 3)
#tkgrid(directoryFrame, sticky="nw",padx = pad.val, pady = pad.y,sticky = "we")
#tkgrid(locationFrame, sticky="w",padx = pad.val, pady = pad.y,sticky = "we")
locationFrame <- tk2labelframe(tb6,text = "script peptide filtering")
directoryFrame <- tk2frame(locationFrame)
onBrowse <- function(){
tclvalue(path3) <- tclvalue(tkgetOpenFile(filetypes = "{{R script} {.R}} {{All files} *}",initialdir=tclvalue(path1),parent = tt2))
}
browseButton <- buttonRcmdr(directoryFrame, text=gettext(question3, domain="R-Rcmdr"), width=path.width, command=onBrowse, borderwidth=3)
locationField <- ttkentry(directoryFrame, width= entryWidth, textvariable=path3)
test<- function(){tclvalue(path3) <- tclvalue(path3) }
test()
locationScroll <- ttkscrollbar(directoryFrame, orient="horizontal",
command=function(...) tkxview(locationField, ...))
tkconfigure(locationField, xscrollcommand=function(...) tkset(locationScroll, ...))
tb6.help.shape.script <- "Use your own shape script, to adjust displacement of peptides that have a certain degree of non measured values. This option replaces the option \"Percentage of allowed NA\"."
tb6.p <- tk2checkbutton(directoryFrame)
tb6.var.shape.script <- tclVar(settings$tb6.var.shape.script)
tkconfigure(tb6.p,variable= tb6.var.shape.script)
#tkgrid(browseButton,locationField, sticky="we",padx = pad.val, pady = pad.y,sticky = "we")
#tkgrid(tk2label(directoryFrame,text="personal shape"),tb6.p,help.button(tb6,"Labeling",tb6.help.shape.script),padx = pad.val,pady = pad.y,sticky = "we")
#tkgrid(directoryFrame, sticky="we",padx = pad.val, pady = pad.y,sticky = "we")
#tkgrid(locationFrame, sticky="we",padx = pad.val, pady = pad.y,sticky = "we")
#tkgrid(tk2label(tb6,text=" "),sticky="w",columnspan = 1,padx = pad.val, pady = pad.y,sticky = "we")
tkfocus(tb6)
#locationFrame <- tk2frame(tb6)
path4 <- tclVar(settings$path4)
locationFrame <- tk2labelframe(tb6,text = "experimental design")
directoryFrame <- tk2frame(locationFrame)
onBrowse <- function(){
tclvalue(path4) <- tclvalue(tkgetOpenFile(filetypes = "{{tab delimited} {.tab}} {{All files} *}", initialdir = tclvalue(path2),parent = tt2))
}
browseButton <- buttonRcmdr(directoryFrame, text=gettext(question4, domain="R-Rcmdr"), width= 10, command=onBrowse)
locationField <- ttkentry(directoryFrame, textvariable=path4,width = 45)
test<- function(){tclvalue(path4) <- tclvalue(path4) }
test()
locationScroll <- ttkscrollbar(directoryFrame, orient="horizontal",
command=function(...) tkxview(locationField, ...))
tkconfigure(locationField)
####
# group
####
temp.fun <- function(){wd <- getwd()
setwd(path2)
hz.show.path()
setwd(wd)
}
cb <- tk2checkbutton(directoryFrame)
tb2.var.groupnorm <- tclVar(settings$tb2.var.groupnorm)#tclVar(settings$tb2.var.groupnorm)
tkconfigure(cb,variable=tb2.var.groupnorm)
tkgrid(browseButton,locationField , tk2button(locationFrame,text = "create",width = 6,command = function(){hz.write.design(as.character(tclvalue(path2)),path2.set$input.file,.data);try(temp.fun)}), sticky="w",padx = pad.val, pady = pad.y,sticky = "we")
tkgrid(tk2label(directoryFrame,text=hz.function.file(function.file,"GSC")[2]),cb,help.button(directoryFrame,hz.function.file(function.file,"GSC")[2] ,hz.function.file(function.file,"GSC")[3]),pady = pad.y,padx = pad.val,sticky = "we")
####
# group filter
####
cb <- tk2checkbutton(directoryFrame)
tb2.var.group.filternorm <- tclVar(settings$tb2.var.group.filternorm)#tclVar(settings$tb2.var.group.filternorm)
tkconfigure(cb,variable=tb2.var.group.filternorm)
tkgrid(tk2label(directoryFrame,text=hz.function.file(function.file,"GSH")[2]),cb,help.button(directoryFrame,hz.function.file(function.file,"GSH")[2] ,hz.function.file(function.file,"GSH")[3]),pady = pad.y,padx = pad.val,sticky = "we")
tkgrid(directoryFrame,padx = pad.val, pady = pad.y,sticky = "we",columnspan =3)
tkgrid(locationFrame,columnspan = 3,padx = pad.val, pady = pad.y,sticky = "we")
#tkgrid(test,sticky ="w",padx = pad.val, pady = pad.y,sticky = "we")
#tkgrid(tk2label(tb2,text=spacer,width = label.width ),columnspan = 3,padx = pad.val, pady = pad.y,sticky = "we")
#tkgrid(tk2label(tb6 ,text=spacer),columnspan = 3,padx = pad.val, pady = pad.y,sticky = "we")
#tkgrid(tk2label(directoryFrame,text="personal shape"),tb6.p,help.button(tb6,"Labeling",tb6.help.shape.script),sticky = "w",columnspan = 3)
######
# save
######
#tkgrid(tk2label(tt2,text=spacer,width = label.width ),columnspan = 3,padx = pad.val, pady = pad.y,sticky = "we")
tt2.settings.var <- c("current settings","no","load standard settings")
tt2.settings.method <- tclVar()
tclvalue(tt2.settings.method) <- settings$tt2.settings.var
comboBox <- ttkcombobox(tt2,values=tt2.settings.var,textvariable = tt2.settings.method,width = 17,state = "readonly")
tkgrid(tklabel(tt2,text = hz.function.file(function.file,"SAVE")[2],font = fontHeading,width = label.width ,background = .bg,justify = "center",compound = "center"),comboBox,help.button(tt2,hz.function.file(function.file,"SAVE")[2], hz.function.file(function.file,"SAVE")[3]),pady = 5)
##############################################################################################################
# End of parameters
##############################################################################################################
Cancel.but <- tk2button(tt2,text="Stop",command=function() {tclvalue(done)<-1;tkdestroy(tt3)})
OK.but <- tk2button(tt2,text="Start",command=function() {tclvalue(done)<-2;tkdestroy(tt3)})
tkgrid(OK.but,Cancel.but,columnspan = 1,pady=5)
tkdestroy(tk.loading)
tkgrid(tt2)
tkbind(tt2, "<Return>",function(x){print("Return");tclvalue(done)<-2 ; tkdestroy(tt3)})
tkbind(tt2, "<Escape>",function(x){print("Return");tclvalue(done)<-1 ; tkdestroy(tt3)})
tkwait.window(tt2)
##############################################################################################################
# End of parameters
##############################################################################################################
tt2.var.expname <- as.character(tclvalue(tt2.var.expname))
settings.old <- settings
binary.rewrite <- function(x){
x <-tclvalue(x)
if(x == 0 | x == "0"){ x <- FALSE}
if(x == 1 | x == "1"){ x <- TRUE}
return(x)
}
#######
# tab1
#######
n.correction = FALSE
settings$tb1.var.protein.intensity <- as.character(tclvalue(tb1.val.protein.intensity))
tb1.val.protein.intensity <- as.character(tclvalue(tb1.val.protein.intensity))
####
settings$tb4.val.raw.values <- as.character(tclvalue(tb4.val.raw.values))
tab.4.var.raw.x <- as.character(tclvalue(tb4.val.raw.values))
sum.of.total <- "sum"
if (tab.4.var.raw.x ==tb4.val.raws[3]){tab.4.var.raw.x <- TRUE; n.correction <- FALSE}else{
if(tab.4.var.raw.x ==tb4.val.raws[2]){tab.4.var.raw.x <- FALSE;n.correction <- TRUE}
if(tab.4.var.raw.x ==tb4.val.raws[1]){tab.4.var.raw.x <- FALSE;n.correction <- FALSE}
if(tab.4.var.raw.x ==tb4.val.raws[4]){tab.4.var.raw.x <- FALSE;n.correction <- FALSE; sum.of.total <- tb4.val.raws[4]}
#if(tab.4.var.raw.x ==tb4.val.raws[3]){tab.4.var.raw.x <- FALSE;n.correction <- TRUE; sum.of.total <- "sum50"}
#if(tab.4.var.raw.x ==tb4.val.raws[4]){tab.4.var.raw.x <- FALSE;n.correction <- FALSE; sum.of.total <- "sum50"}
}
tab.4.var.raw.x <- as.character((tab.4.var.raw.x))
######
settings$tb1.val.replicates.cp <- as.character(tclvalue(tb1.val.replicates.cp))
tb1.val.replicates.cp <- as.character(tclvalue(tb1.val.replicates.cp))
if (tb1.val.replicates.cp =="1"){tb1.val.replicates.cp <- TRUE}else{tb1.val.replicates.cp <- FALSE}
tb1.val.replicates.cp <- as.character((tb1.val.replicates.cp))
settings$tb1.val.replicates <- as.character(tclvalue(tb1.val.replicates))
tb1.val.replicates <- as.character(tclvalue(tb1.val.replicates))
if (tb1.val.replicates =="1"){tb1.val.replicates <- FALSE}else{tb1.val.replicates <- TRUE}
tb1.val.replicates <- as.character((tb1.val.replicates))
######
settings$tb1.duplicates.var = as.character(tclvalue(tb1.val.pep.duplicates))
tb1.val.pep.duplicates = as.character(tclvalue(tb1.val.pep.duplicates))
#####
settings$tb1.val.conrev <- as.character(tclvalue(tb1.val.conrev))
tb1.val.conrev <- as.character(tclvalue(tb1.val.conrev))
if (tb1.val.conrev =="1"){tb1.val.conrev <- TRUE}else{tb1.val.conrev <- FALSE}
tb1.val.conrev <- as.character((tb1.val.conrev))
#######
# tab2
#######
tt2.experiment.name <- as.character(tclvalue(tt2.experiment.name))
##
settings$tb2.var.rownorm <- as.character(tclvalue(tb2.var.rownorm))
tb2.var.rownorm <- as.character(tclvalue(tb2.var.rownorm))
if (tb2.var.rownorm=="1"){tb2.var.rownorm <- TRUE}else{tb2.var.rownorm = FALSE}
tb2.var.rownorm <- as.character(tb2.var.rownorm)
#settings$tb3.var.phospho <- as.character(tclvalue(tb3.var.phospho))
#tb3.var.phospho <- as.character(tclvalue(tb3.var.phospho))
#if (tb3.var.phospho =="1"){tb3.var.phospho <- TRUE}else{tb3.var.phospho <- FALSE}
#tb3.var.phospho <- as.character(tb3.var.phospho)
settings$tb2.val.score <- as.numeric(tclvalue(tb2.val.score))
tb2.val.score <- as.numeric(tclvalue(tb2.val.score))
if(is.na(tb2.val.score)){tb2.val.score <- 0}
settings$tb2.var.groupnorm <- tclvalue(tb2.var.groupnorm)
settings$tb2.var.group.filternorm <- tclvalue((tb2.var.group.filternorm))
settings$tb2.norm.method <- tclvalue(tb2.val.norm.method)
#######
# tab3
#######
try( tb3.var.phospho <- tclvalue(tb3.var.phospho))
try(settings$tb3.phospho <- tb3.var.phospho)
#tb3.var.phospho.protein <- FALSE
#tb3.var.phospho <- FALSE
if((tb3.var.phospho) == tb3.phospho[1]){
tb3.var.phospho <- FALSE
tb3.var.phospho.protein <- FALSE
}else{
if((tb3.var.phospho) == tb3.phospho[2]){
tb3.var.phospho <- TRUE
tb3.var.phospho.protein <- FALSE
}else{
if((tb3.var.phospho) == tb3.phospho[3]){
tb3.var.phospho <- TRUE
tb3.var.phospho.protein <- TRUE
}else{
tb3.var.phospho <- FALSE
tb3.var.phospho.protein <- FALSE
}
}
}
settings$tb3.outlier <- as.character(tclvalue(tb3.var.outlier))
tb3.var.outlier <- as.character(tclvalue(tb3.var.outlier))
if(tb3.var.outlier == tb3.outlier[1] ){tb3.var.outlier ="NA"}
if(tb3.var.outlier == tb3.outlier[2] ){tb3.var.outlier ="row"}
if(tb3.var.outlier == tb3.outlier[3] ){tb3.var.outlier ="all.below"}
if(tb3.var.outlier == tb3.outlier[4] ){tb3.var.outlier ="top.3"}
settings$tb2.var.db <- tclvalue(tb2.var.db)
db.dat <- paste("cRackerSequence-",tclvalue(tb2.var.db),sep = "")
### if exclusion of redundant = TRUE
settings$tb2.var.red.pep <- as.character(tclvalue(tb2.var.red.pep))
tb2.var.red.pep <- as.character(tclvalue(tb2.var.red.pep))
if (tb2.var.red.pep =="1"){tb2.var.red.pep <- TRUE}else{tb2.var.red.pep <- FALSE}
tb2.var.red.pep <- as.character((tb2.var.red.pep))
### if exclusion of redundant = TRUE
settings$tb2.var.shape <- as.numeric(tclvalue(tb2.var.shape))
## if max qu exclu
settings$tb2.var.red.pep.mq <- as.character(tclvalue(tb2.var.red.pep.mq))
tb2.var.red.pep.mq <- as.character(tclvalue(tb2.var.red.pep.mq))
if (tb2.var.red.pep.mq =="1"){tb2.var.red.pep.mq <- TRUE}else{tb2.var.red.pep.mq <- FALSE}
tb2.var.red.pep.mq <- as.character(tb2.var.red.pep.mq)
## zero treat
settings$tb3.val.zero.treat <- as.numeric(tclvalue(tb3.val.zero.treat))
tb3.val.zero.treat <- as.numeric(tclvalue(tb3.val.zero.treat))
### build matrix
## plot.only
#######
# tab4
#######
settings$tb4.quant.method <- as.character(tclvalue(tb4.quant.method ))
tb4.quant.method <- as.character(tclvalue(tb4.quant.method ))
print("tb4.quant.method")
if(tb4.quant.method == "cbn"){tb4.var.cbn <- "1";tb4.val.n15 <- "0"}
if(tb4.quant.method == "15n"){tb4.var.cbn <- "0";tb4.val.n15 <- "1"}
if(tb4.quant.method == "lf"){tb4.var.cbn <- "0";tb4.val.n15 <- "0"}
print(tb4.quant.method)
## Reference Protein
settings$tb4.val.cbn.prot <- as.character(tclvalue(tb4.val.cbn.prot))
if(tb4.var.cbn == "1"){tb4.val.cbn.prot <- as.character(tclvalue(tb4.val.cbn.prot)) }else{tb4.val.cbn.prot <- NULL}
## norm ref value
tb4.var2.cbn <- as.character(tclvalue(tb4.var2.cbn))
if(tb4.var2.cbn == "1"){tb4.var2.cbn <- TRUE }else{tb4.var2.cbn <- FALSE}
settings$tb4.val.cbn.shape <- as.numeric(tclvalue(tb4.val.cbn.shape))
## 15n
if(tb4.val.n15 == "1"){tb4.val.n15 <- TRUE }else{tb4.val.n15 <- FALSE}
########
settings$tb4.val.n15.log <- as.character(tclvalue(tb4.val.n15.log))
tb4.val.n15.log <- as.character(tclvalue(tb4.val.n15.log))
if(tb4.val.n15.log == "1"){tb4.val.n15.log <- TRUE }else{tb4.val.n15.log <- FALSE}
#######
settings$tb4.var.n15.log.correction <- tclvalue(tb4.val.n15.log.correction)#
tb4.val.n15.log.correction <- tclvalue(tb4.val.n15.log.correction)#
#######
settings$tb4.val.ratio <- as.numeric(tclvalue(tb4.val.ratio))
tb4.val.ratio <- as.numeric(tclvalue(tb4.val.ratio))
######
#######
# tab5
#######
tb5.val.kmeans <- tclvalue(tb5.val.kmeans)
if(tb5.val.kmeans!= "auto"){
tb5.val.kmeans <- as.numeric(tb5.val.kmeans)
if(is.na(tb5.val.kmeans)){
tb5.val.kmeans <- "auto"
}
}
settings$tb5.val.kmeans <- tb5.val.kmeans
cracker <- as.character(tclvalue(path1))
path.data <- as.character(tclvalue(path2))
path.script.shape <- as.character(tclvalue(path3))
exp.design <- as.character(tclvalue(path4))
settings$tb6.var.shape.script <- as.character(tclvalue(tb6.var.shape.script))
tb6.var.shape.script <- as.character(tclvalue(tb6.var.shape.script))
if (tb6.var.shape.script=="1"){tb6.var.shape.script <- "TRUE"}else{tb6.var.shape.script = "FALSE"}
tb6.var.shape.script <- as.character(tb6.var.shape.script )
settings$tb5.var.p.adjust<- tclvalue(tb5.val.p.adjust)
tb5.val.p.adjust<- tclvalue(tb5.val.p.adjust)
settings$tb5.val.anova.p <- as.numeric(tclvalue(tb5.val.anova.p ))
tb5.val.anova.p <- as.numeric(tclvalue(tb5.val.anova.p ))
settings$tb5.var.do.go <- binary.rewrite(tb5.var.do.go)
settings$tb5.go.term.list <- tclvalue(tb5.val.go.term.list)
settings$tb5.val.volcano <- tclvalue(tb5.val.volcano)
settings$tb5.var.color.plots <- tclvalue(tb5.var.color.plots)
settings$tb5.var.graphic.type <- tclvalue(tb5.var.graphic.type)
settings$tb5.val.volcano <- tclvalue(tb5.val.volcano)
settings$tb5.do.cor <- tclvalue(tb5.val.do.cor)
settings$tb5.var.log2.ratio.thres <- tclvalue(tb5.var.log2.ratio.thres )
tb5.nb.2.fl.bp.frame.val.plot.type<- tclvalue(tb5.nb.2.fl.bp.frame.val.plot.type)
settings$tb5.nb.2.fl.bp.frame.val.plot.type <- tb5.nb.2.fl.bp.frame.val.plot.type
if(tb5.nb.2.fl.bp.frame.val.plot.type == tb5.1.2.fl.bp.frame.plot.type.var[1] ){
barpl = TRUE
time.grouped = FALSE
lineplot.beside = FALSE
}
if(tb5.nb.2.fl.bp.frame.val.plot.type == tb5.1.2.fl.bp.frame.plot.type.var[2] ){
barpl = TRUE
time.grouped = TRUE
lineplot.beside = FALSE
}
if(tb5.nb.2.fl.bp.frame.val.plot.type == tb5.1.2.fl.bp.frame.plot.type.var[3] ){
barpl = FALSE
time.grouped = FALSE
lineplot.beside = FALSE
}
if(tb5.nb.2.fl.bp.frame.val.plot.type == tb5.1.2.fl.bp.frame.plot.type.var[4] ){
barpl = FALSE
time.grouped = TRUE
lineplot.beside = FALSE
}
if(tb5.nb.2.fl.bp.frame.val.plot.type == tb5.1.2.fl.bp.frame.plot.type.var[5] ){
barpl = FALSE
time.grouped = TRUE
lineplot.beside = TRUE
}
settings$tb5.nb.2.fl.bp.frame.var.xlab <- tclvalue(tb5.1.2.fl.bp.frame.var.xlab)
settings$tb5.val.cluster.method <- tclvalue(tb5.val.cluster.method)
if(tclvalue(tb5.val.cluster.method) == "hclust"){
hclust.groups = TRUE}else{hclust.groups <- FALSE}
settings$tb5.val.anova.log2 <-tclvalue(tb5.val.anova.log2)
settings$val.onetailed.ttest <- tclvalue(tb5.val.onetailed.ttest)
####
# tb7
####
####
# rewrite settings
###
print("save settings")
try(
if(1==1&tclvalue(done) !=3){
tt2.settings.method <- as.character(tclvalue(tt2.settings.method))
if(tt2.settings.method == tt2.settings.var[1]){
try( save(settings,file= paste(path1.backup,"/settings.Rdata",sep ="")))
}
if(tt2.settings.method == tt2.settings.var[2]){}
if(tt2.settings.method == tt2.settings.var[3]){
load(paste(path1.backup,"/settings-standard.Rdata",sep =""))
try(save( settings,file = paste(path1.backup,"/settings.Rdata",sep ="")))
tclvalue(done) <- 4
}
})
print("saved settings")
#######
# returning list
#######
print(tclvalue(done))
if(tclvalue(done) == 2){ return(ReadAffy(
celfile.path = list(
settings = settings,
cracker = cracker,
path.data = path.data,
db = db.dat,
path.shape = path.script.shape,
msquant = tt2.experiment.name,
peptidenorm = tb1.val.replicates.cp,
raw = tb1.val.replicates,
peptidemerge = tb1.val.protein.intensity,
dupli.val = tb1.val.pep.duplicates,
ex.conrev = tb1.val.conrev,
use.raw = tab.4.var.raw.x,
norm.method = tclvalue(tb2.val.norm.method),
sum.of.total = sum.of.total,
score = tb2.val.score,
row.norm = tb2.var.rownorm,
shape = as.numeric(tclvalue(tb2.var.shape )),
expname = tt2.var.expname,
exclu = tb2.var.red.pep,
maxq.exclu = tb2.var.red.pep.mq,
group.norm = binary.rewrite(tb2.var.groupnorm),
group.filter = binary.rewrite(tb2.var.group.filternorm),
outlier = tb3.var.outlier,
phospho = tb3.var.phospho,
phospho.protein = tb3.var.phospho.protein,
zero.treat = tb3.val.zero.treat,
build.matrix = TRUE,#tb3.var.build.matrix,
#plot.only = binary.rewrite(tb3.var.plot.only),
plot.only = tclvalue(path5),
cbn.prot = tb4.val.cbn.prot,
shape.prot.norm = as.numeric(tclvalue(tb4.val.cbn.shape)),
n.correction = n.correction,
#position = tkwm.geometry(tb1)
N15 = tb4.val.n15,
row.target.norm = tb4.var2.cbn,
n15.log2 = tb4.val.n15.log ,
n15.correct.method = tb4.val.n15.log.correction,
n15.correct.expect = tb4.val.ratio,
centers = tb5.val.kmeans,
p.adjust.method = tb5.val.p.adjust,
p.value = tb5.val.anova.p,
log2.test = binary.rewrite(tb5.val.anova.log2),
volcano = binary.rewrite(tb5.val.volcano),
onetailed.ttest = binary.rewrite(tb5.val.onetailed.ttest),
graphic.type = tclvalue(tb5.var.graphic.type),
ratio.thres = tclvalue(tb5.var.log2.ratio.thres),
do.GO = binary.rewrite(tb5.var.do.go),#tb5.do.go.m
go.library = paste("cRackerMapping-",tclvalue(tb5.val.go.term.list),sep = ""),
do.cor = tclvalue(tb5.val.do.cor),
do.network = binary.rewrite(tb5.var.do.network),
color.plots = tclvalue(tb5.var.color.plots),
barpl = barpl,
time.grouped = time.grouped,
lineplot.beside = lineplot.beside,
x.xlab = as.character(tclvalue(tb5.1.2.fl.bp.frame.var.xlab)),
exp.design = exp.design,
hclust.groups = hclust.groups,
script.shape = tb6.var.shape.script ,
quant.method = tb4.quant.method,
calc.empai = FALSE,
empai.sd = FALSE,
empai.from.msms = FALSE,
empai.pep.length= 6,
empai.reference = ""
)))}else{
if(tclvalue(done) == 3){return("switch")}
if(tclvalue(done) == 1){return("stopped")}
if(tclvalue(done) == 4){return("reload")}
}
}
#print(gui.input<- hz.read.parameters(path1 =("/Users/henno/cracker/pkg/data/"),path2 = "",path2.set = list(settings = "",2,3),.data = ""))
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hz.read.parameters <-
function( image.path = NULL,
build.matrix = "1",
.bg = "lightgrey",
path2,
path2.set,
.data,
path1
) {
##d9d9d9
#.bg = "red"
require(tcltk)
require(tcltk2)
print("test")
done <- tclVar(0)
print("starting GUI")
( path1.backup <- path1)
( path2.backup <- path2)
print("test")
print(getwd())
license.text <- paste( "Copyright (C) <2011> \n<Henrik Zauber; Max Planck Institute for Molecular Plant Physiology>\n
This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with this program. If not, see <http://www.gnu.org/licenses/>")
try( function.file <- read.csv(paste(path1,"/help-file.csv",sep = ""), stringsAsFactors = FALSE)
)
if(!exists("function.file")){
try( function.file <- read.csv(paste(path1,"/help-file.csv.gz",sep = ""), stringsAsFactors = FALSE)
)
}
if(!exists("function.file")){ function.file <- ""
}else{
print("Read function.file successfully.")
}
tk2font.set("TkDefaultFont",settings= "-family Tahoma -size 10 -weight normal")
#.bg.col <- "#efefef"
fontHeading <- tkfont.create(family = "Tahoma",size=10,weight="bold")
hz.path.set <- function(title.q){
fileDir<-tclvalue(tkchooseDirectory(title=title.q))
return(ReadAffy(celfile.path = fileDir))}
########################################################################################
### GUI START #############################################################################
########################################################################################
spacer <- " "
tt3 <- tktoplevel(bg = .bg)
tkwm.title(tt3,"cRacker")
tkwm.resizable(tt3, "FALSE","FALSE")
topMenu <- tk2menu(tt3,background = .bg)
tkconfigure(tt3,menu=topMenu,background = .bg)
fileMenu <- tk2menu(topMenu,tearoff=FALSE,background = .bg)
go.libraryMenu <- tk2menu(topMenu,tearoff=FALSE,background = .bg)
tt2 <- tkframe(tt3,bg = .bg)
if(is.null(image.path) == FALSE& 1==0){
.wd.image <- getwd()
setwd(image.path)
error.try <- class(try( .cra.img <- tkimage.create("photo", file=paste(path1,"/cRacker-logo-grey.pnm",sep = ""))))
if(error.try == "try-error"){.cra.img <- ""}
.cra <- tk2label(tt2,image = .cra.img,background = .bg)
setwd(.wd.image)
image.file <- TRUE
}else{image.file <- FALSE}
########
# loading:
#######
tk.loading <- tktoplevel(background = .bg)
tkfocus(tk.loading)
tkgrid(tklabel(tk.loading,text="Loading, please be patient",background = .bg))
if(image.file){
tkgrid(tklabel(tk.loading,image=.cra.img,background = .bg))
}
#load settings-files
if(path2.set$settings == "default" | !exists("path2.set")|exists(".data2")){
print("loaded settings")
try(load(paste(path1,"/settings.Rdata",sep = "")))
print("test")
}else{
print("loaded selected settings")
try(load(path2.set$settings))
}
#tkwm.geometry(tt2,"445x410+20+0")
if(!exists("settings")){
settings <- hz.cracker.default.settings()
}
info <- paste(license.text)
#tkgrid(image.button(tt2,"cRacker",info,image = .cra.img,fgcol = "white",bgcol = "white",size = 15,bf = "bold"),columnspan = 2,pady = 5)
label.width = 35
#####
# top down level
#####
# libraries
# GO
list.files.mapping <- list.files(paste((path1),sep = ""))
list.files.mapping <- list.files.mapping[grep("^cRackerMapping",list.files.mapping)]
tkadd( go.libraryMenu,
"command",
label="Add",
command=function(){
try(hz.go.input(path1))
tkmessageBox(title="Message",message="Finished Import\nPlease restart cRacker!",icon="warning",type="ok")
},background = .bg)
tkadd(go.libraryMenu,"command",label="Remove",
command=function(){hz.remove.data(type = "^cRackerMapping",path1 =tclvalue(path1))},background = .bg)
tkadd(fileMenu,"cascade",label="Mappings",menu=go.libraryMenu,background = .bg)
#emPAI
empai.libraryMenu <- tk2menu(topMenu,tearoff=FALSE)
tkadd( empai.libraryMenu,
"command",
label="Add",
command=function(){
try(hz.library.fasta(path1))
tkmessageBox(title="Message",message="Finished Import\nPlease restart cRacker!",icon="warning",type="ok")
})
tkadd(empai.libraryMenu,"command",label="Remove", command=function(){hz.remove.data(type = "^cRackerSequence|^cRackerEmPAI",path1 =tclvalue(path1))},background = .bg)
tkadd(fileMenu,"cascade",label="Protein Sequence library",menu=empai.libraryMenu,background = .bg)
tkadd(topMenu,"cascade",label="Libraries",menu=fileMenu,background = .bg)
######################
# choose quantitation type
######################
entryInit <- "ms-analysis"
entryWidth <- 20
question <- "Experiment Name"
tt2.var.expname <- tclVar(paste(entryInit))
textEntryWidget <- tkentry(tt2,width=paste(entryWidth),textvariable= tt2.var.expname)
if(image.file){image.input<- image.button(tt2,"cRacker",info,image = .cra.img,fgcol = "white",bgcol = "white",size = 3,bf = "bold")}else{
image.input <- help.button(tt2,"cRacker",buttontext = "cRacker")
}
tkgrid(tk2label(tt2,text=question,font = fontHeading,background = .bg,width = label.width),textEntryWidget, image.input,pady = 5,padx = 5)
tt2.experiment.name <- tclVar("1.x")
tkgrid(tk2separator(tt2),sticky = "we",columnspan = 3,pady = 5)
######
# Quantitation method
######
quant.method.button <- "switch to emPAI"
empai.button <- tk2button(tt2,text=quant.method.button ,command=function() {tkdestroy(tt3);path1 <- path1.backup;path2 <- path2.backup;tclvalue(done) <- 3})
tkgrid(tklabel(tt2,text= hz.function.file(function.file,"QM")[2] ,font = fontHeading,width = label.width ,background = .bg,justify = "center",compound = "center"),empai.button,help.button(tt2,hz.function.file(function.file,"QM")[2], hz.function.file(function.file,"QM")[3]))
tkgrid(tklabel(tt2,text=">> IonIntensities <<",fg = "red",bg = .bg),sticky = "s",columnspan = 3)
########################################################################################################################
### TAB
########################################################################################################################
tabs <- c(
tab1 <- "Main",
tab2 <- "Peptides -> Protein",
tab3 <- "Extra",
tab4 <- "Quantitation Mode",
tab5 <- "Statistics",
tab5.1 <- "Plotting",
tab6 <- "Paths"
)
nb <- tk2notebook(tt2, tabs = tabs) # starts notebook
# Make non selected tabs a little darker
#tcl("ttk::style", "configure", "TNotebook.Pane", forground = "blue",background="skyblue3")
#tcl("ttk::style", "map", "TNotebook.Tab", background=c("active", "skyblue"))
#tcl("ttk::style", "map", "TNotebook.Tab", background=c("active", "skyblue"))
#tcl("ttk::style", "configure", "TNotebook.Pane", forground=c("red"))
#tcl("ttk::style", "configure", "TNotebook.Pane", forground=c("red"))
tkgrid(nb,columnspan = 3,padx=5)
# first tab:
tb1 <- tk2notetab(nb, tab1)
tb2 <- tk2notetab(nb, tab2)
tb3 <- tk2notetab(nb, tab3)
tb4 <- tk2notetab(nb, tab4)
tb5 <- tk2notetab(nb, tab5)
tb5.1 <- tk2notetab(nb, tab5.1)
tb6 <- tk2notetab(nb, tab6)
pad.val <- 2
pad.y <- 2
tcl("ttk::style", "configure", "TNotebook", background=.bg)
tcl("ttk::style", "configure", "TNotebook.Tab",foreground = "black", background=.bg)
#tcl("ttk::style", "map", "TNotebook.Tab",foreground = c("focus", "red"))
tcl("ttk::style", "map", "TNotebook.Tab",foreground = c("active", "red"))
#tcl("ttk::style", "configure", "TNotebook", foreground = .bg,background=.bg)
#tcl("ttk::style", "configure", "TNotebook.Pane", background=.bg)
# Make non selected tabs a little darker
#tcl("ttk::style", "configure", "TNotebook.Pane", forground = "blue",background="skyblue3")
#tcl("ttk::style", "map", "TNotebook.Tab", background=c("active", "skyblue"))
#tcl("ttk::style", "map", "TNotebook.Tab", background=c("active", "skyblue"))
tcl("ttk::style", "configure", "TNotebook.Tab", foreground=c("black"))
tcl("ttk::style", "configure", "TNotebook.Pane", foreground=c("red"))
######
# Replicates
######
cb3 <- tk2checkbutton(tb1)
tb1.val.replicates <- tclVar(settings$tb1.val.replicates)
tkconfigure(cb3,variable=tb1.val.replicates)
tkgrid(tk2label(tb1,text= hz.function.file(function.file,"AR")[2],font = fontHeading,width = label.width ),cb3,help.button(tb1,hz.function.file(function.file,"AR")[2] ,hz.function.file(function.file,"AR")[3]),padx = pad.val, pady = pad.y,sticky = "we")
######
# common peptides:
######
help.tb1.replicate.cp <- "Only active if \"Replicates\" option is used. An additional normalization factor is created based on the mean relative change of common peptides between replicate samples."
cb4 <- tk2checkbutton(tb1)
tb1.val.replicates.cp <- tclVar(0)#settings$tb1.val.replicates.cp
tkconfigure(cb4,variable=tb1.val.replicates.cp)
#tkgrid(tk2label(tb1,text=title.t <- "normalise on common peptides",width = label.width),cb4,help.button(tb1,title.t ,help.tb1.replicate.cp),padx = pad.val, pady = pad.y,sticky = "we")
#tkgrid(tk2label(tb1,text=spacer, width = label.width ),padx = pad.val, pady = pad.y,columnspan = 3)
######
# merging Peptides
######
####
# protein.intensity
####
#tkgrid(tk2label(tb1,text=spacer,width = label.width ),columnspan = 3,padx = pad.val, pady = pad.y,sticky = "we")
tb1.var.protein.intensity <- c("mean","median","sum")
tb1.val.protein.intensity <- tclVar()
tclvalue(tb1.val.protein.intensity) <- settings$tb1.var.protein.intensity
comboBox <- ttkcombobox(tb1,values=tb1.var.protein.intensity,textvariable = tb1.val.protein.intensity,width = 17,state = "readonly")
tkgrid(tk2label(tb1,text = hz.function.file(function.file,"AM")[2],font = fontHeading,width = label.width ),comboBox,help.button(tb1,hz.function.file(function.file,"AM")[2], hz.function.file(function.file,"AM")[3]),padx = pad.val, pady = pad.y,sticky = "we")
####
# duplicate peptides
####
#tkgrid(tk2label(tb1,text=spacer,width = label.width ),columnspan = 3,padx = pad.val, pady = pad.y,sticky = "we")
tb1.duplicates.var <- c("mean","sum","max","min","exclude")
tb1.val.pep.duplicates <- tclVar()
tclvalue(tb1.val.pep.duplicates) <- settings$tb1.duplicates.var
comboBox <- ttkcombobox(tb1,values=tb1.duplicates.var,textvariable = tb1.val.pep.duplicates,width = 17,state = "readonly")
tkgrid(tk2label(tb1,text=hz.function.file(function.file,"PD")[2],font = fontHeading,width = label.width ),comboBox,help.button(tb1,hz.function.file(function.file,"PD")[2] , hz.function.file(function.file,"PD")[3]),padx = pad.val, pady = pad.y,sticky = "we")
######
# contaminants
######
cb4 <- tk2checkbutton(tb1)
tb1.val.conrev <- tclVar(settings$tb1.val.conrev)
tkconfigure(cb4,variable=tb1.val.conrev)
tkgrid(tk2label(tb1,text= hz.function.file(function.file,"ExCR")[2],font = fontHeading,width = label.width ),cb4,help.button(tb1,hz.function.file(function.file,"ExCR")[2] ,hz.function.file(function.file,"ExCR")[3]),padx = pad.val, pady = pad.y,sticky = "we")
#######
# tab 2
#######
pad.val <- pad.val
######
# score
######
entryWidth <- 40
tb2.val.score <- tclVar(settings$tb2.val.score)
textEntryWidget <- tkentry(tb2,width=paste(entryWidth),textvariable=tb2.val.score,width = 20)
tkgrid(tk2label(tb2,text=hz.function.file(function.file,"PST")[2],font = fontHeading,width = label.width ),textEntryWidget,help.button(tb2,hz.function.file(function.file,"PST")[2],hz.function.file(function.file,"PST")[3]),padx = pad.val, pady = pad.y,sticky = "we")
######
# Tab2
#####
####
# normalization
####
cb <- tk2checkbutton(tb2)
tb2.var.rownorm <- tclVar(settings$tb2.var.rownorm)
tkconfigure(cb,variable=tb2.var.rownorm)
tkgrid(tk2label(tb2,text=hz.function.file(function.file,"SaS")[2],font = fontHeading,width = label.width ),cb,help.button(tb2,hz.function.file(function.file,"SaS")[2] ,hz.function.file(function.file,"SaS")[3]),padx = pad.val, pady = pad.y,sticky = "we")
####
# norm.method
####
tb2.var.norm.method <- c("mean","median","z-score")
tb2.val.norm.method <- tclVar()
tclvalue(tb2.val.norm.method) <- settings$tb2.norm.method
comboBox <- ttkcombobox(tb2,values=tb2.var.norm.method,textvariable = tb2.val.norm.method,width = 17,state = "readonly")
tkgrid(tk2label(tb2,text=hz.function.file(function.file,"SM")[2],font = fontHeading,width = label.width ),comboBox,help.button(tb2,hz.function.file(function.file,"SM")[2] , hz.function.file(function.file,"SM")[3]),padx = pad.val, pady = pad.y,sticky = "nwe")
####
# shape
####
tb2.var.shape <- tclVar(settings$tb2.var.shape)
SliderValueLabel <- tk2label(tb2,text=tclvalue(tb2.var.shape))
tkconfigure(SliderValueLabel,textvariable= tb2.var.shape)
slider <- tkscale(tb2, from=0, to=100,
variable= tb2.var.shape,
orient="horizontal",
resolution = 1,
showvalue = T,
length = 136,
bg = .bg
)
tkgrid(tk2label(tb2,text=hz.function.file(function.file,"PoaN")[2],font = fontHeading,width = label.width ),slider,help.button(tb2,hz.function.file(function.file,"PoaN")[2] ,hz.function.file(function.file,"PoaN")[3]),padx = pad.val, pady = pad.y,sticky = "we")
#####
# redundant pep
#####
cb <- tk2checkbutton(tb2)
tb2.var.red.pep <- tclVar(settings$tb2.var.red.pep)
tkconfigure(cb,variable=tb2.var.red.pep)
tkgrid(tk2label(tb2,text=hz.function.file(function.file,"EoRP")[2] ,font = fontHeading,width = label.width),cb,help.button(tb2,hz.function.file(function.file,"EoRP")[2] ,hz.function.file(function.file,"EoRP")[3]),sticky = "s",padx = pad.val, pady = pad.y,sticky = "we")
tb2.var.db <- tclVar()
tclvalue(tb2.var.db) <- settings$tb2.var.db
list.files.data <- list.files(paste(path1,sep = ""))
list.files.data <- list.files.data[grep("cRackerSequence-",list.files.data,fixed = T)]
list.files.data <- substring(list.files.data,17,nchar(list.files.data))
db <- as.character(list.files.data)
comboBox <- ttkcombobox(tb2,values=db,textvariable = tb2.var.db,width = 17,state = "readonly")
tkgrid(tk2label(tb2,text="search duplicates for exclusion"),comboBox,padx = pad.val, pady = pad.y,sticky = "we")
cbmq <- tk2checkbutton(tb2)
tb2.var.red.pep.mq <- tclVar(settings$tb2.var.red.pep.mq)
tkconfigure(cbmq,variable=tb2.var.red.pep.mq)
tkgrid(tk2label(tb2,text="use list info for exclusion" ),cbmq,sticky = "we")
# tab3
######
####
# PHospho
####
# tb4.4 <- tk2checkbutton(tb3)#
# tb3.var.phospho <- tclVar(settings$tb3.var.phospho)
#tkconfigure(tb4.4,variable=tb3.var.phospho)
#tkgrid(tk2label(tb3,text=hz.function.file(function.file,"PP")[2],font = fontHeading,width = label.width ),tb4.4,help.button(tb3,hz.function.file(function.file,"PP")[2] ,hz.function.file(function.file,"PP")[3]),padx = pad.val, pady = pad.y,sticky = "we")
tb3.phospho <- c("none","peptide based analysis","protein based analysis")
tb3.var.phospho <- tclVar()
tclvalue(tb3.var.phospho) <- settings$tb3.phospho
comboBox <- ttkcombobox(tb3,values=tb3.phospho,textvariable = tb3.var.phospho,width = 17,state = "readonly")
tkgrid(tk2label(tb3,text=hz.function.file(function.file,"PP")[2],font = fontHeading,width = label.width ),comboBox,help.button(tb3,hz.function.file(function.file,"PP")[2] , hz.function.file(function.file,"PP")[3]),padx = pad.val, pady = pad.y,sticky = "we")
######
# outlier
######
#tkgrid(tk2label(tb3,text=spacer,width = label.width ),columnspan = 3,padx = pad.val, pady = pad.y,sticky = "we")
tb3.outlier <- c("none","outside both whiskers","outside lower whisker","top 3")
tb3.var.outlier <- tclVar()
tclvalue(tb3.var.outlier) <- settings$tb3.outlier
comboBox <- ttkcombobox(tb3,values=tb3.outlier,textvariable = tb3.var.outlier,width = 17,state = "readonly")
tkgrid(tk2label(tb3,text=hz.function.file(function.file,"OE")[2],font = fontHeading,width = label.width ),comboBox,help.button(tb3,hz.function.file(function.file,"OE")[2] , hz.function.file(function.file,"OE")[3]),padx = pad.val, pady = pad.y,sticky = "we")
######
# zero handling
######
entryWidth <- 5
tb3.val.zero.treat <- tclVar(paste(settings$tb3.val.zero.treat ))
onArgEdit <- function () {
if (is.integer(tb3.val.zero.treat) == FALSE){
tclvalue(tb3.val.zero.treat) <- tclvalue(tb3.val.zero.treat)
tkconfigure(textEntryWidget, textvarible= tb3.val.zero.treat)
}
return(tclVar(is.integer(tb3.val.zero.treat))) # Must return TRUE to accept edition!
}
textEntryWidget <- tkentry(tb3,width=paste(entryWidth),textvariable= tb3.val.zero.treat,width = 19,validate = "none",validatecommand = onArgEdit)
tkgrid(tk2label(tb3,text=hz.function.file(function.file,"ZH")[2],font = fontHeading,width = label.width),textEntryWidget,help.button(tb3,hz.function.file(function.file,"ZH")[2], hz.function.file(function.file,"ZH")[3]),padx = pad.val, pady = pad.y,sticky = "we" )
####
# TAB4
pad.val = pad.val
pad.y = 0.5
######
# raw values
######
tb4.rb1 <- tk2radiobutton(tb4)
tb4.rb2 <- tk2radiobutton(tb4)
tb4.rb3 <- tk2radiobutton(tb4)
tb4.rb4 <- tk2radiobutton(tb4)
tb4.quant.method <- tclVar(settings$tb4.quant.method)
tkconfigure(tb4.rb1,variable=tb4.quant.method,value="lf")
tkconfigure(tb4.rb2,variable=tb4.quant.method,value="cbn")
tkconfigure(tb4.rb3,variable=tb4.quant.method,value="15n")
entryWidth <- 17
help.tb4.raw.values <-
tb4.val.raws <- c( "fraction of total (fot)",
"fot plus n correction (fotn)",#"fot 50", #"fotn 50",
"no normalization","equal.peptides")
tb4.val.raw.values <- tclVar()
tclvalue(tb4.val.raw.values ) <- settings$tb4.val.raw.values
if(length(grep(settings$tb4.val.raw.values,tb4.val.raws,fixed = TRUE))==0){tclvalue(tb4.val.raw.values ) <- tb4.val.raws[1]}
comboBox <- ttkcombobox(tb4,values=tb4.val.raws ,textvariable = tb4.val.raw.values, width = entryWidth ,state = "readonly")
tkgrid(tk2label(tb4,text=hz.function.file(function.file,"LF")[2],font = fontHeading,width = label.width),tb4.rb1,help.button(tb4,hz.function.file(function.file,"LF")[2], hz.function.file(function.file,"LF")[3]),padx = pad.val, pady = pad.y,sticky = "we")
tkgrid(tk2label(tb4,text = ""),comboBox,tk2label(tb4,text = ""))
#####
# CBN
#####
tb4.p <- tk2checkbutton(tb4)
tb4.var.cbn <- tclVar(settings$tb4.var.cbn)
tkconfigure(tb4.p,variable= tb4.var.cbn)
tkgrid(tk2label(tb4,text=hz.function.file(function.file,"RPN")[2],font = fontHeading,width = label.width),tb4.rb2,help.button(tb4,hz.function.file(function.file,"RPN")[2],hz.function.file(function.file,"RPN")[3]),padx = pad.val, pady = pad.y ,columnspan = 1,sticky = "we")
tb4.help1.1 <- "Choose if factor is used on raw data, or on scaled peptide data."
tb4.p2 <- tk2checkbutton(tb4)
tb4.var2.cbn <- tclVar(settings$tb4.var2.cbn)
tkconfigure(tb4.p2,variable= tb4.var2.cbn)
#tkgrid(tk2label(tb4,text="use on scaled peptides"),tb4.p2,help.button(tb4,"row norm",tb4.help1.1),padx = pad.val, pady = pad.y,sticky = "we")
question <- "Protein:"
tb4.help2.cbn <- "Define the Accession code of your reference Protein. Default is BSA."
tb4.val.cbn.prot <- tclVar(paste(settings$tb4.val.cbn.prot))
tb4.textEntryWidget <- tkentry(tb4,width=paste(entryWidth+3),textvariable=tb4.val.cbn.prot)
tkgrid(tk2label(tb4,text=hz.function.file(function.file,"RP")[2]),tb4.textEntryWidget,help.button(tb4,hz.function.file(function.file,"RP")[2],hz.function.file(function.file,"RP")[3]),padx = pad.val, pady = pad.y,sticky = "we")
####
# norm.prot shape
####
tb4.val.cbn.shape <- tclVar(settings$tb4.val.cbn.shape)
SliderValueLabel.tb4 <- tk2label(tb4,text=as.character(tclvalue(tb4.val.cbn.shape)))
tkconfigure(SliderValueLabel.tb4,textvariable=tb4.val.cbn.shape)
slider.tb4 <- tkscale(tb4, from=0, to=100,
variable=tb4.val.cbn.shape,
orient="horizontal",
resolution = 1,
showvalue = T
, length =paste(entryWidth+120),
bg = .bg)
tkgrid(tk2label(tb4,text = hz.function.file(function.file,"RPNS")[2] ),slider.tb4,help.button(tb4,hz.function.file(function.file,"RPNS")[2] ,hz.function.file(function.file,"RPNS")[3] ))
#tkgrid(tk2label(tb4,text=spacer),columnspan = 3)
#######
# tb4.val.n15
######
tb4.tb4.val.n15.p <- tk2checkbutton(tb4)
tb4.val.n15 <- tclVar(settings$tb4.val.n15)
tkconfigure(tb4.tb4.val.n15.p,variable= tb4.val.n15)
tkgrid(tk2label(tb4,text=hz.function.file(function.file,"LN")[2] ,font = fontHeading,width = label.width ),tb4.rb3,help.button(tb4,hz.function.file(function.file,"LN")[2] ,hz.function.file(function.file,"LN")[3] ),padx = pad.val, pady = pad.y,sticky = "we")
#####
# log
#####
tb4.tb4.val.n15.log.p <- tk2checkbutton(tb4)
tb4.val.n15.log <- tclVar(settings$tb4.val.n15.log)
tkconfigure(tb4.tb4.val.n15.log.p,variable= tb4.val.n15.log)
tkgrid(tk2label(tb4,text=hz.function.file(function.file,"LOG")[2] ),tb4.tb4.val.n15.log.p,help.button(tb4,hz.function.file(function.file,"LOG")[2],hz.function.file(function.file,"LOG")[3]),padx = pad.val, pady = pad.y,sticky = "we")
####
# n15.log.correction
####
tb4.var.n15.log.correction <- c("none","mean","median")
tb4.val.n15.log.correction <- tclVar()
tclvalue(tb4.val.n15.log.correction) <- settings$tb4.var.n15.log.correction
comboBox <- ttkcombobox(tb4,values=tb4.var.n15.log.correction,textvariable = tb4.val.n15.log.correction,width = 17,state = "readonly")
tkgrid(tk2label(tb4,text=hz.function.file(function.file,"CorLOG")[2]),comboBox,help.button(tb4,hz.function.file(function.file,"CorLOG")[2] , hz.function.file(function.file,"CorLOG")[3]),padx = pad.val, pady = pad.y,sticky = "we")
######
# ratio
######
######
entryWidth <- 5
tb4.val.ratio <- tclVar(paste(settings$tb4.val.ratio ))
onArgEdit <- function () {
if (is.integer(tb4.val.ratio) == FALSE){
tclvalue(tb4.val.ratio) <- settings$tb4.val.ratio
tkconfigure(textEntryWidget, textvariable= tb4.val.ratio)
}
return(tclVar(is.integer(tb4.val.ratio))) # Must return TRUE to accept edition!
}
textEntryWidget <- tkentry(tb4,width=paste(entryWidth),textvariable= tb4.val.ratio,width = 19,validate = "none",validatecommand = onArgEdit)
tkgrid(tk2label(tb4,text=hz.function.file(function.file,"ERLU")[2]),textEntryWidget,help.button(tb4,hz.function.file(function.file,"ERLU")[2], hz.function.file(function.file,"ERLU")[3]),padx = pad.val, pady = pad.y,sticky = "we" )
#tb5.1 <- tk2notebook(tb5, tabs = nb.tb5.names<- c("settings","plots")) # starts notebook
#tb5 <- tk2notetab(tb5.1, nb.tb5.names[1] )
#tb5.1.2 <- tk2notetab(tb5.1, nb.tb5.names[2] )
#tkgrid(tb5.1)
####
# cluster.method
####
tkframe.kmeans <- tk2frame(tb5 )
entryWidth <- 5
tb5.val.kmeans <- tclVar(paste(settings$tb5.val.kmeans ))
onArgEdit <- function () {
if (is.integer(tb5.val.kmeans) == FALSE){
tclvalue(tb5.val.kmeans) <- settings$tb5.val.kmeans
tkconfigure(textEntryWidget, textvariable= tb5.val.kmeans)
}
return(tclVar(is.integer(tb5.val.kmeans))) # Must return TRUE to accept edition!
}
textEntryWidget <- tkentry(tb5,width=paste(entryWidth),textvariable= tb5.val.kmeans,width = 5,validate = "none",validatecommand = onArgEdit)
tb5.var.cluster.method <- c("k-Means","hclust")
tb5.val.cluster.method <- tclVar()
tclvalue(tb5.val.cluster.method) <- settings$tb5.val.cluster.method
comboBox <- ttkcombobox(tkframe.kmeans,values=tb5.var.cluster.method,textvariable = tb5.val.cluster.method,width = 8,state = "readonly")
tkgrid(tk2label(tkframe.kmeans,text = "Clustering ",font = fontHeading,),comboBox,tk2label(tkframe.kmeans,text = " , cluster:"),columnspan = 3)
tkgrid(tkframe.kmeans, textEntryWidget,help.button(tb5,hz.function.file(function.file,"MTC")[2], hz.function.file(function.file,"MTC")[3]),padx = pad.val, pady = pad.y,sticky = "we")
#stop()
#tkgrid(tk2label(tb5,text=hz.function.file(function.file,"MTC")[2]),comboBox,help.button(tb5,hz.function.file(function.file,"MTC")[2], hz.function.file(function.file,"MTC")[3]),padx = pad.val, pady = pad.y,sticky = "we")
######
# anova.p
######
tkframe.anova.log2 <- tk2frame(tb5 )
anova.log.cb <- tk2checkbutton(tkframe.anova.log2)
tb5.val.anova.log2 <- tclVar(settings$tb5.val.anova.log2)
tkconfigure(anova.log.cb,variable=tb5.val.anova.log2)
entryWidth <- 5
tb5.val.anova.p <- tclVar(paste(settings$tb5.val.anova.p))
onArgEdit <- function () {
if (is.integer(tb5.val.anova.p) == FALSE){
tclvalue(tb5.val.anova.p) <- settings$tb5.val.anova.p
tkconfigure(textEntryWidget, textvariable= tb5.val.anova.p)
}
return(tclVar(is.integer(tb5.val.anova.p))) # Must return TRUE to accept edition!
}
textEntryWidget <- tkentry(tb5,width=paste(entryWidth),textvariable= tb5.val.anova.p,width = 19,validate = "none",validatecommand = onArgEdit)
tkgrid(tk2label(tkframe.anova.log2,text = paste(hz.function.file(function.file,"PANOVA")[2],"(log2"),font = fontHeading),anova.log.cb,tk2label(tkframe.anova.log2,text = "):",font= fontHeading),columnspan = 3,sticky = "we" )
tkgrid(tkframe.anova.log2,textEntryWidget,help.button(tb5,hz.function.file(function.file,"PANOVA")[2],hz.function.file(function.file,"PANOVA")[3]),padx = pad.val, pady = pad.y,sticky = "we" )
####
# p.adjust
####
tb5.var.p.adjust <- c("holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none")
tb5.val.p.adjust <- tclVar()
tclvalue(tb5.val.p.adjust) <- settings$tb5.var.p.adjust
comboBox <- ttkcombobox(tb5,values=tb5.var.p.adjust,textvariable = tb5.val.p.adjust,width = 17,state = "readonly")
tkgrid(tk2label(tb5,text=hz.function.file(function.file,"MTC")[2]),comboBox,help.button(tb5,hz.function.file(function.file,"MTC")[2], hz.function.file(function.file,"MTC")[3]),padx = pad.val, pady = pad.y,sticky = "we")
######
# onetailed
######
cb3 <- tk2checkbutton(tb5)
tb5.val.onetailed.ttest <- tclVar(settings$val.onetailed.ttest)
tkconfigure(cb3,variable=tb5.val.onetailed.ttest)
tkgrid(tk2label(tb5,text="Include one tailed t-test",width = label.width ),cb3,help.button(tb5,"Include one tailed t-test" ,""),padx = pad.val, pady = pad.y,sticky = "we")
####
# do.go
####
tb5.do.go.m <- tk2checkbutton(tb5)
tb5.var.do.go <- tclVar(settings$tb5.var.do.go)
tkconfigure(tb5.do.go.m,variable=tb5.var.do.go)
#tkgrid(tk2label(tb5,text=hz.function.file(function.file,"MAP")[2],font = fontHeading,width = label.width ),tb5.do.go.m,help.button(tb5,hz.function.file(function.file,"MAP")[2],hz.function.file(function.file,"MAP")[3]),padx = pad.val, pady = pad.y,sticky = "we")
####
# path Goterm
####
path1 <- tclVar(path1)
tb5.var.go.term.list <-c("none",as.character(gsub("^cRackerMapping-","",list.files.mapping)))
tb5.val.go.term.list <- tclVar()
tclvalue(tb5.val.go.term.list) <- settings$tb5.go.term.list
comboBox <- ttkcombobox(tb5,values=tb5.var.go.term.list,textvariable = tb5.val.go.term.list,width = 17,state = "readonly")
tkgrid(tk2label(tb5,text=hz.function.file(function.file,"MAPL")[2],font = fontHeading,width = label.width ),comboBox,help.button(tb5,hz.function.file(function.file,"MAPL")[2], hz.function.file(function.file,"MAPL")[3]),padx = pad.val, pady = pad.y,sticky = "we")
####
# Correlation Matrix
####
tb5.do.cor.help <-
"Choose the type of correlation for creating a cross correlation list."
#tkgrid(tk2label(tb5,text=spacer,width = label.width ),columnspan = 3,padx = pad.val, pady = pad.y,sticky = "we")
tb5.do.cor <- c("pearson", "kendall", "spearman","none")
tb5.val.do.cor <- tclVar()
tclvalue(tb5.val.do.cor) <- settings$tb5.do.cor
comboBox <- ttkcombobox(tb5,values=tb5.do.cor,textvariable = tb5.val.do.cor,width = 17,state = "readonly")
tkgrid(tk2label(tb5,text=hz.function.file(function.file,"CA")[2],font = fontHeading,width = label.width ),comboBox,help.button(tb5,hz.function.file(function.file,"CA")[2], hz.function.file(function.file,"CA")[3]),padx = pad.val, pady = pad.y,sticky = "we")
############
# network
############
do.network <- 0
tb5.do.network.m <- tk2checkbutton(tb5)
tb5.var.do.network <- tclVar(0)#tclVar(settings$tb5.var.do.network)
tkconfigure(tb5.do.network.m,variable=tb5.var.do.network)
#tkgrid(tk2label(tb5,text=hz.function.file(function.file,"PN")[2]),tb5.do.network.m,help.button(tb5,hz.function.file(function.file,"PN")[2],hz.function.file(function.file,"PN")[3]),padx = pad.val, pady = pad.y,sticky = "we")
######
# volcano
######
cb3 <- tk2checkbutton(tb5)
tb5.val.volcano <- tclVar(settings$tb5.val.volcano)
tkconfigure(cb3,variable=tb5.val.volcano)
tkgrid(tk2label(tb5,text=hz.function.file(function.file,"VP")[2],font = fontHeading,width = label.width ),cb3,help.button(tb5,hz.function.file(function.file,"VP")[2] ,hz.function.file(function.file,"VP")[3]),padx = pad.val, pady = pad.y,sticky = "we")
##########
# log2 ratio threshold
#########
tb5.var.log2.ratio.thres <- tclVar(settings$tb5.var.log2.ratio.thres)
SliderValueLabel <- tk2label(tb5,text=tclvalue(tb5.var.log2.ratio.thres))
tkconfigure(SliderValueLabel,textvariable= tb5.var.log2.ratio.thres)
slider <- tkscale( tb5, from=0, to=5,
variable= tb5.var.log2.ratio.thres,
orient="horizontal",
resolution = 0.1,
showvalue = T,
length = 136,
bg = .bg
)
tkgrid(tk2label(tb5,text=hz.function.file(function.file,"LRT")[2]),slider,help.button(tb5,hz.function.file(function.file,"LRT")[2] ,hz.function.file(function.file,"LRT")[3]),padx = pad.val, pady = pad.y,sticky = "we")
##########################################################################
########## tb5.1.2.fl.bp <- tk2labelframe(tb5.1.2) statistics
###########################################################################
label.width.temp <- 22
pad.y <- 2
pad.val <- 2
tb5.1.2.fl.bp <- tk2labelframe(tb5.1,text = "type of single protein plots")
tb5.1.2.fl.bp.frame <- tk2frame(tb5.1.2.fl.bp )
#############
parent.placeholder <- tb5.1.2.fl.bp.frame
tb5.1.2.fl.bp.frame.plot.type.var <- c("barplot","grouped barplot (based on time column)","lineplot","time series (all in one)","time series (single plot)")
tb5.nb.2.fl.bp.frame.val.plot.type <- tclVar()
tclvalue(tb5.nb.2.fl.bp.frame.val.plot.type) <- settings$tb5.nb.2.fl.bp.frame.val.plot.type
comboBox <- ttkcombobox(parent.placeholder,values=tb5.1.2.fl.bp.frame.plot.type.var,textvariable = tb5.nb.2.fl.bp.frame.val.plot.type,width = .width.temp<- 30,state = "readonly")
print("test")
tkgrid(tk2label(parent.placeholder,text=hz.function.file(function.file,"SPPT")[2],font = fontHeading,width = label.width.temp ),comboBox,help.button(parent.placeholder,hz.function.file(function.file,"SPPT")[2] , hz.function.file(function.file,"SPPT")[3]),padx = pad.val, pady = pad.y,sticky = "wen")
##############
tb5.1.2.fl.bp.frame.var.xlab <- tclVar(settings$tb5.nb.2.fl.bp.frame.var.xlab)
textEntryWidget <- tk2entry(parent.placeholder,width=.width.temp,textvariable= tb5.1.2.fl.bp.frame.var.xlab)
tkgrid(tk2label(parent.placeholder,text=hz.function.file(function.file,"XL")[2],font = fontHeading,width = label.width.temp),textEntryWidget, help.button(parent.placeholder,hz.function.file(function.file,"XL")[2] , hz.function.file(function.file,"XL")[3]),padx = pad.val, pady = pad.y,sticky = "wen")
##############
#############
tkgrid(tb5.1.2.fl.bp.frame,sticky = "wen",padx = pad.val, pady = pad.y,sticky = "we")
tkgrid(tb5.1.2.fl.bp,columnspan = 3, sticky = "wen",padx = pad.val, pady = pad.y,sticky = "we")
########
########
##########################################################################################
############
# color plots
############
#settings$tb5.color.plots <- "rainbow"
tb5.help.color.plots <- "Select the color mode for plot output."
#tkgrid(tk2label(tb5,text=spacer,width = label.width ),columnspan = 3,padx = pad.val, pady = pad.y,sticky = "we")
tb5.color.plots <- c("rainbow","colorblind","greytone")
tb5.var.color.plots <- tclVar()
tclvalue(tb5.var.color.plots) <- settings$tb5.var.color.plots
comboBox <- ttkcombobox(tb5.1,values=tb5.color.plots,textvariable = tb5.var.color.plots,width = 17,state = "readonly")
tkgrid(tk2label(tb5.1,text=hz.function.file(function.file,"CM")[2],font = fontHeading,width = label.width ),comboBox,help.button(tb5.1,hz.function.file(function.file,"CM")[2], hz.function.file(function.file,"CM")[3]),padx = pad.val, pady = pad.y,sticky = "we")
############
# graphic.type
############
#settings$tb5.graphic.type <- "rainbow"
tb5.help.graphic.type <- "Graphic type defines the graphic type, that is used for graphic output."
print("test")
#tkgrid(tk2label(tb5,text=spacer,width = label.width ),columnspan = 3,padx = pad.val, pady = pad.y,sticky = "we")
tb5.graphic.type <- c("pdf","eps")
tb5.var.graphic.type <- tclVar()
tclvalue(tb5.var.graphic.type) <- settings$tb5.var.graphic.type
comboBox <- ttkcombobox(tb5.1,values=tb5.graphic.type,textvariable = tb5.var.graphic.type,width = 17,state = "readonly")
tkgrid(tk2label(tb5.1,text=hz.function.file(function.file,"GT")[2],font = fontHeading,width = label.width ),comboBox,help.button(tb5.1,hz.function.file(function.file,"GT")[2], hz.function.file(function.file,"GT")[3]),padx = pad.val, pady = pad.y,sticky = "we")
####
# only plotting
####
plot.only <- FALSE
locationFrame <- tk2frame(tb5.1)
path5 <- tclVar("")
buttonRcmdr <- function(..., borderwidth, fg, foreground, relief) ttkbutton(...)
onBrowse <- function(){
tclvalue(path5) <- tclvalue(tkgetOpenFile(filetypes = "{{Rdata} {.Rdata}} {{All files} *}", initialdir = tclvalue(path2),parent = tt2))
}
browseButton <- buttonRcmdr(tb5.1, text=gettext("Browse", domain="R-Rcmdr"), width= 6, command=onBrowse, borderwidth=3)
locationField <- ttkentry(tb5.1, width=entryWidth, textvariable=path5)
locationScroll <- ttkscrollbar(tb5.1, orient="horizontal",
command=function(...) tkxview(tb5.1, ...))
tkconfigure(locationField, xscrollcommand=function(...) tkset(locationScroll, ...))
tkgrid(tk2label(tb5.1,text= hz.function.file(function.file,"SfR")[2],font = fontHeading,width = label.width ),locationField, browseButton,sticky = "we",padx = pad.val,pady = pad.y,sticky = "we")
######
# tab6
######
pad.val = 1
tkgrid(tk2label(tb6,text="Paths",font = fontHeading),sticky="w",padx = pad.val, pady = pad.y,sticky = "we")
#tkgrid(tk2label(tb6,text="selected folders:"),sticky="w",padx = pad.val, pady = pad.y,sticky = "we")
#path1 <- tclVar(path1)
path2 <- tclVar(path2)
path3 <- tclVar(paste(as.character(tclvalue(path1)),"scripts/script.shape.R",sep = ""))
buttonRcmdr <- function(..., borderwidth, fg, foreground, relief) ttkbutton(...)
entryWidth <- 37
question1 <- "Browse:"
question2 <- "data:"
question3 <- "Browse"
question4 <- "Browse"
path.width <- 16
locationFrame <- tk2labelframe(tb6,text = "cRacker path")
path1 <- path1
directoryFrame <- tk2frame(locationFrame)
onBrowse <- function(){
tclvalue(path1) <- tclvalue(tkchooseDirectory(initialdir = tclvalue(path1),parent = tt2))
}
browseButton <- buttonRcmdr(directoryFrame, text=gettext(question1, domain="R-Rcmdr"), width= path.width, command=onBrowse, borderwidth=3)
locationField <- ttkentry(directoryFrame, width=entryWidth, textvariable=path1)
test<- function(){tclvalue(path1) <- tclvalue(path1) }
test()
locationScroll <- ttkscrollbar(directoryFrame, orient="horizontal",
command=function(...) tkxview(locationField, ...))
tkconfigure(locationField, xscrollcommand=function(...) tkset(locationScroll, ...))
#tkgrid(browseButton,locationField, sticky="w",padx = pad.val, pady = pad.y,sticky = "we")
#tkgrid(directoryFrame, sticky="nw",padx = pad.val, pady = pad.y,sticky = "we")
#tkgrid(locationFrame, sticky="w",columnspan = 3,padx = pad.val, pady = pad.y,sticky = "we")
onBrowse <- function(){
tclvalue(path2) <- tclvalue(tkchooseDirectory(initialdir = tclvalue(path2),parent = tt2))
}
browseButton <- buttonRcmdr(directoryFrame, text=gettext(question2, domain="R-Rcmdr"), width=path.width, command=onBrowse, borderwidth=3)
locationField <- ttkentry(directoryFrame, width= entryWidth, textvariable=path2)
test<- function(){tclvalue(path2) <- tclvalue(path2) }
test()
locationScroll <- ttkscrollbar(directoryFrame, orient="horizontal",
command=function(...) tkxview(locationField, ...))
tkconfigure(locationField, xscrollcommand=function(...) tkset(locationScroll, ...))
#tkgrid(browseButton,locationField, sticky="w",padx = pad.val, pady = pad.y,sticky = "we")
#tkgrid(directoryFrame, sticky="nw",padx = pad.val, pady = pad.y,sticky = "we")
#tkgrid(locationFrame, sticky="we",padx = pad.val, pady = pad.y,sticky = "we")
####
#checkmark for personal shaping
###
#tkgrid(tk2label(tb6,text=" "),sticky="w",columnspan = 1,padx = pad.val, pady = pad.y,sticky = "we")
#locationFrame <- tk2labelframe(tb6)
#directoryFrame <- tk2frame(locationFrame)
path.labelframe <- tk2labelframe(tb6,text = "cRacker path")
path.frame <- tk2frame(path.labelframe)
path1.input <- tclvalue(path1)
path2.input <- tclvalue(path2)
tkgrid(tk2label(path.frame,text = "cracker:"),tk2label(tb6,text = hz.brake.strings(path1.input,70)),sticky = "wn")
tkgrid(tk2label(path.frame,text = "data path:"),tk2label(tb6,text = hz.brake.strings(path2.input,70)),sticky = "wn")
tkgrid(path.frame)
tkgrid(path.labelframe,sticky="ew",columnspan = 3)
#tkgrid(tk2label(tb6,text = "data path:"),tk2label(tb6,text = tclvalue(path2)))
tkgrid(tk2label(tb6,text="Advanced",font = fontHeading),sticky="w",padx = pad.val, pady = pad.y,sticky = "we")
#tkgrid(tk2label(directoryFrame,text="personal shape"),tb6.p,help.button(tb6,"Labeling",tb6.help.shape.script),sticky = "w",columnspan = 3)
#tkgrid(directoryFrame, sticky="nw",padx = pad.val, pady = pad.y,sticky = "we")
#tkgrid(locationFrame, sticky="w",padx = pad.val, pady = pad.y,sticky = "we")
locationFrame <- tk2labelframe(tb6,text = "script peptide filtering")
directoryFrame <- tk2frame(locationFrame)
onBrowse <- function(){
tclvalue(path3) <- tclvalue(tkgetOpenFile(filetypes = "{{R script} {.R}} {{All files} *}",initialdir=tclvalue(path1),parent = tt2))
}
browseButton <- buttonRcmdr(directoryFrame, text=gettext(question3, domain="R-Rcmdr"), width=path.width, command=onBrowse, borderwidth=3)
locationField <- ttkentry(directoryFrame, width= entryWidth, textvariable=path3)
test<- function(){tclvalue(path3) <- tclvalue(path3) }
test()
locationScroll <- ttkscrollbar(directoryFrame, orient="horizontal",
command=function(...) tkxview(locationField, ...))
tkconfigure(locationField, xscrollcommand=function(...) tkset(locationScroll, ...))
tb6.help.shape.script <- "Use your own shape script, to adjust displacement of peptides that have a certain degree of non measured values. This option replaces the option \"Percentage of allowed NA\"."
tb6.p <- tk2checkbutton(directoryFrame)
tb6.var.shape.script <- tclVar(settings$tb6.var.shape.script)
tkconfigure(tb6.p,variable= tb6.var.shape.script)
#tkgrid(browseButton,locationField, sticky="we",padx = pad.val, pady = pad.y,sticky = "we")
#tkgrid(tk2label(directoryFrame,text="personal shape"),tb6.p,help.button(tb6,"Labeling",tb6.help.shape.script),padx = pad.val,pady = pad.y,sticky = "we")
#tkgrid(directoryFrame, sticky="we",padx = pad.val, pady = pad.y,sticky = "we")
#tkgrid(locationFrame, sticky="we",padx = pad.val, pady = pad.y,sticky = "we")
#tkgrid(tk2label(tb6,text=" "),sticky="w",columnspan = 1,padx = pad.val, pady = pad.y,sticky = "we")
tkfocus(tb6)
#locationFrame <- tk2frame(tb6)
path4 <- tclVar(settings$path4)
locationFrame <- tk2labelframe(tb6,text = "experimental design")
directoryFrame <- tk2frame(locationFrame)
onBrowse <- function(){
tclvalue(path4) <- tclvalue(tkgetOpenFile(filetypes = "{{tab delimited} {.tab}} {{All files} *}", initialdir = tclvalue(path2),parent = tt2))
}
browseButton <- buttonRcmdr(directoryFrame, text=gettext(question4, domain="R-Rcmdr"), width= 10, command=onBrowse)
locationField <- ttkentry(directoryFrame, textvariable=path4,width = 45)
test<- function(){tclvalue(path4) <- tclvalue(path4) }
test()
locationScroll <- ttkscrollbar(directoryFrame, orient="horizontal",
command=function(...) tkxview(locationField, ...))
tkconfigure(locationField)
####
# group
####
temp.fun <- function(){wd <- getwd()
setwd(path2)
hz.show.path()
setwd(wd)
}
cb <- tk2checkbutton(directoryFrame)
tb2.var.groupnorm <- tclVar(settings$tb2.var.groupnorm)#tclVar(settings$tb2.var.groupnorm)
tkconfigure(cb,variable=tb2.var.groupnorm)
tkgrid(browseButton,locationField , tk2button(locationFrame,text = "create",width = 6,command = function(){hz.write.design(as.character(tclvalue(path2)),path2.set$input.file,.data);try(temp.fun)}), sticky="w",padx = pad.val, pady = pad.y,sticky = "we")
tkgrid(tk2label(directoryFrame,text=hz.function.file(function.file,"GSC")[2]),cb,help.button(directoryFrame,hz.function.file(function.file,"GSC")[2] ,hz.function.file(function.file,"GSC")[3]),pady = pad.y,padx = pad.val,sticky = "we")
####
# group filter
####
cb <- tk2checkbutton(directoryFrame)
tb2.var.group.filternorm <- tclVar(settings$tb2.var.group.filternorm)#tclVar(settings$tb2.var.group.filternorm)
tkconfigure(cb,variable=tb2.var.group.filternorm)
tkgrid(tk2label(directoryFrame,text=hz.function.file(function.file,"GSH")[2]),cb,help.button(directoryFrame,hz.function.file(function.file,"GSH")[2] ,hz.function.file(function.file,"GSH")[3]),pady = pad.y,padx = pad.val,sticky = "we")
tkgrid(directoryFrame,padx = pad.val, pady = pad.y,sticky = "we",columnspan =3)
tkgrid(locationFrame,columnspan = 3,padx = pad.val, pady = pad.y,sticky = "we")
#tkgrid(test,sticky ="w",padx = pad.val, pady = pad.y,sticky = "we")
#tkgrid(tk2label(tb2,text=spacer,width = label.width ),columnspan = 3,padx = pad.val, pady = pad.y,sticky = "we")
#tkgrid(tk2label(tb6 ,text=spacer),columnspan = 3,padx = pad.val, pady = pad.y,sticky = "we")
#tkgrid(tk2label(directoryFrame,text="personal shape"),tb6.p,help.button(tb6,"Labeling",tb6.help.shape.script),sticky = "w",columnspan = 3)
######
# save
######
#tkgrid(tk2label(tt2,text=spacer,width = label.width ),columnspan = 3,padx = pad.val, pady = pad.y,sticky = "we")
tt2.settings.var <- c("current settings","no","load standard settings")
tt2.settings.method <- tclVar()
tclvalue(tt2.settings.method) <- settings$tt2.settings.var
comboBox <- ttkcombobox(tt2,values=tt2.settings.var,textvariable = tt2.settings.method,width = 17,state = "readonly")
tkgrid(tklabel(tt2,text = hz.function.file(function.file,"SAVE")[2],font = fontHeading,width = label.width ,background = .bg,justify = "center",compound = "center"),comboBox,help.button(tt2,hz.function.file(function.file,"SAVE")[2], hz.function.file(function.file,"SAVE")[3]),pady = 5)
##############################################################################################################
# End of parameters
##############################################################################################################
Cancel.but <- tk2button(tt2,text="Stop",command=function() {tclvalue(done)<-1;tkdestroy(tt3)})
OK.but <- tk2button(tt2,text="Start",command=function() {tclvalue(done)<-2;tkdestroy(tt3)})
tkgrid(OK.but,Cancel.but,columnspan = 1,pady=5)
tkdestroy(tk.loading)
tkgrid(tt2)
tkbind(tt2, "<Return>",function(x){print("Return");tclvalue(done)<-2 ; tkdestroy(tt3)})
tkbind(tt2, "<Escape>",function(x){print("Return");tclvalue(done)<-1 ; tkdestroy(tt3)})
tkwait.window(tt2)
##############################################################################################################
# End of parameters
##############################################################################################################
tt2.var.expname <- as.character(tclvalue(tt2.var.expname))
settings.old <- settings
binary.rewrite <- function(x){
x <-tclvalue(x)
if(x == 0 | x == "0"){ x <- FALSE}
if(x == 1 | x == "1"){ x <- TRUE}
return(x)
}
#######
# tab1
#######
n.correction = FALSE
settings$tb1.var.protein.intensity <- as.character(tclvalue(tb1.val.protein.intensity))
tb1.val.protein.intensity <- as.character(tclvalue(tb1.val.protein.intensity))
####
settings$tb4.val.raw.values <- as.character(tclvalue(tb4.val.raw.values))
tab.4.var.raw.x <- as.character(tclvalue(tb4.val.raw.values))
sum.of.total <- "sum"
if (tab.4.var.raw.x ==tb4.val.raws[3]){tab.4.var.raw.x <- TRUE; n.correction <- FALSE}else{
if(tab.4.var.raw.x ==tb4.val.raws[2]){tab.4.var.raw.x <- FALSE;n.correction <- TRUE}
if(tab.4.var.raw.x ==tb4.val.raws[1]){tab.4.var.raw.x <- FALSE;n.correction <- FALSE}
if(tab.4.var.raw.x ==tb4.val.raws[4]){tab.4.var.raw.x <- FALSE;n.correction <- FALSE; sum.of.total <- tb4.val.raws[4]}
#if(tab.4.var.raw.x ==tb4.val.raws[3]){tab.4.var.raw.x <- FALSE;n.correction <- TRUE; sum.of.total <- "sum50"}
#if(tab.4.var.raw.x ==tb4.val.raws[4]){tab.4.var.raw.x <- FALSE;n.correction <- FALSE; sum.of.total <- "sum50"}
}
tab.4.var.raw.x <- as.character((tab.4.var.raw.x))
######
settings$tb1.val.replicates.cp <- as.character(tclvalue(tb1.val.replicates.cp))
tb1.val.replicates.cp <- as.character(tclvalue(tb1.val.replicates.cp))
if (tb1.val.replicates.cp =="1"){tb1.val.replicates.cp <- TRUE}else{tb1.val.replicates.cp <- FALSE}
tb1.val.replicates.cp <- as.character((tb1.val.replicates.cp))
settings$tb1.val.replicates <- as.character(tclvalue(tb1.val.replicates))
tb1.val.replicates <- as.character(tclvalue(tb1.val.replicates))
if (tb1.val.replicates =="1"){tb1.val.replicates <- FALSE}else{tb1.val.replicates <- TRUE}
tb1.val.replicates <- as.character((tb1.val.replicates))
######
settings$tb1.duplicates.var = as.character(tclvalue(tb1.val.pep.duplicates))
tb1.val.pep.duplicates = as.character(tclvalue(tb1.val.pep.duplicates))
#####
settings$tb1.val.conrev <- as.character(tclvalue(tb1.val.conrev))
tb1.val.conrev <- as.character(tclvalue(tb1.val.conrev))
if (tb1.val.conrev =="1"){tb1.val.conrev <- TRUE}else{tb1.val.conrev <- FALSE}
tb1.val.conrev <- as.character((tb1.val.conrev))
#######
# tab2
#######
tt2.experiment.name <- as.character(tclvalue(tt2.experiment.name))
##
settings$tb2.var.rownorm <- as.character(tclvalue(tb2.var.rownorm))
tb2.var.rownorm <- as.character(tclvalue(tb2.var.rownorm))
if (tb2.var.rownorm=="1"){tb2.var.rownorm <- TRUE}else{tb2.var.rownorm = FALSE}
tb2.var.rownorm <- as.character(tb2.var.rownorm)
#settings$tb3.var.phospho <- as.character(tclvalue(tb3.var.phospho))
#tb3.var.phospho <- as.character(tclvalue(tb3.var.phospho))
#if (tb3.var.phospho =="1"){tb3.var.phospho <- TRUE}else{tb3.var.phospho <- FALSE}
#tb3.var.phospho <- as.character(tb3.var.phospho)
settings$tb2.val.score <- as.numeric(tclvalue(tb2.val.score))
tb2.val.score <- as.numeric(tclvalue(tb2.val.score))
if(is.na(tb2.val.score)){tb2.val.score <- 0}
settings$tb2.var.groupnorm <- tclvalue(tb2.var.groupnorm)
settings$tb2.var.group.filternorm <- tclvalue((tb2.var.group.filternorm))
settings$tb2.norm.method <- tclvalue(tb2.val.norm.method)
#######
# tab3
#######
try( tb3.var.phospho <- tclvalue(tb3.var.phospho))
try(settings$tb3.phospho <- tb3.var.phospho)
#tb3.var.phospho.protein <- FALSE
#tb3.var.phospho <- FALSE
if((tb3.var.phospho) == tb3.phospho[1]){
tb3.var.phospho <- FALSE
tb3.var.phospho.protein <- FALSE
}else{
if((tb3.var.phospho) == tb3.phospho[2]){
tb3.var.phospho <- TRUE
tb3.var.phospho.protein <- FALSE
}else{
if((tb3.var.phospho) == tb3.phospho[3]){
tb3.var.phospho <- TRUE
tb3.var.phospho.protein <- TRUE
}else{
tb3.var.phospho <- FALSE
tb3.var.phospho.protein <- FALSE
}
}
}
settings$tb3.outlier <- as.character(tclvalue(tb3.var.outlier))
tb3.var.outlier <- as.character(tclvalue(tb3.var.outlier))
if(tb3.var.outlier == tb3.outlier[1] ){tb3.var.outlier ="NA"}
if(tb3.var.outlier == tb3.outlier[2] ){tb3.var.outlier ="row"}
if(tb3.var.outlier == tb3.outlier[3] ){tb3.var.outlier ="all.below"}
if(tb3.var.outlier == tb3.outlier[4] ){tb3.var.outlier ="top.3"}
settings$tb2.var.db <- tclvalue(tb2.var.db)
db.dat <- paste("cRackerSequence-",tclvalue(tb2.var.db),sep = "")
### if exclusion of redundant = TRUE
settings$tb2.var.red.pep <- as.character(tclvalue(tb2.var.red.pep))
tb2.var.red.pep <- as.character(tclvalue(tb2.var.red.pep))
if (tb2.var.red.pep =="1"){tb2.var.red.pep <- TRUE}else{tb2.var.red.pep <- FALSE}
tb2.var.red.pep <- as.character((tb2.var.red.pep))
### if exclusion of redundant = TRUE
settings$tb2.var.shape <- as.numeric(tclvalue(tb2.var.shape))
## if max qu exclu
settings$tb2.var.red.pep.mq <- as.character(tclvalue(tb2.var.red.pep.mq))
tb2.var.red.pep.mq <- as.character(tclvalue(tb2.var.red.pep.mq))
if (tb2.var.red.pep.mq =="1"){tb2.var.red.pep.mq <- TRUE}else{tb2.var.red.pep.mq <- FALSE}
tb2.var.red.pep.mq <- as.character(tb2.var.red.pep.mq)
## zero treat
settings$tb3.val.zero.treat <- as.numeric(tclvalue(tb3.val.zero.treat))
tb3.val.zero.treat <- as.numeric(tclvalue(tb3.val.zero.treat))
### build matrix
## plot.only
#######
# tab4
#######
settings$tb4.quant.method <- as.character(tclvalue(tb4.quant.method ))
tb4.quant.method <- as.character(tclvalue(tb4.quant.method ))
print("tb4.quant.method")
if(tb4.quant.method == "cbn"){tb4.var.cbn <- "1";tb4.val.n15 <- "0"}
if(tb4.quant.method == "15n"){tb4.var.cbn <- "0";tb4.val.n15 <- "1"}
if(tb4.quant.method == "lf"){tb4.var.cbn <- "0";tb4.val.n15 <- "0"}
print(tb4.quant.method)
## Reference Protein
settings$tb4.val.cbn.prot <- as.character(tclvalue(tb4.val.cbn.prot))
if(tb4.var.cbn == "1"){tb4.val.cbn.prot <- as.character(tclvalue(tb4.val.cbn.prot)) }else{tb4.val.cbn.prot <- NULL}
## norm ref value
tb4.var2.cbn <- as.character(tclvalue(tb4.var2.cbn))
if(tb4.var2.cbn == "1"){tb4.var2.cbn <- TRUE }else{tb4.var2.cbn <- FALSE}
settings$tb4.val.cbn.shape <- as.numeric(tclvalue(tb4.val.cbn.shape))
## 15n
if(tb4.val.n15 == "1"){tb4.val.n15 <- TRUE }else{tb4.val.n15 <- FALSE}
########
settings$tb4.val.n15.log <- as.character(tclvalue(tb4.val.n15.log))
tb4.val.n15.log <- as.character(tclvalue(tb4.val.n15.log))
if(tb4.val.n15.log == "1"){tb4.val.n15.log <- TRUE }else{tb4.val.n15.log <- FALSE}
#######
settings$tb4.var.n15.log.correction <- tclvalue(tb4.val.n15.log.correction)#
tb4.val.n15.log.correction <- tclvalue(tb4.val.n15.log.correction)#
#######
settings$tb4.val.ratio <- as.numeric(tclvalue(tb4.val.ratio))
tb4.val.ratio <- as.numeric(tclvalue(tb4.val.ratio))
######
#######
# tab5
#######
tb5.val.kmeans <- tclvalue(tb5.val.kmeans)
if(tb5.val.kmeans!= "auto"){
tb5.val.kmeans <- as.numeric(tb5.val.kmeans)
if(is.na(tb5.val.kmeans)){
tb5.val.kmeans <- "auto"
}
}
settings$tb5.val.kmeans <- tb5.val.kmeans
cracker <- as.character(tclvalue(path1))
path.data <- as.character(tclvalue(path2))
path.script.shape <- as.character(tclvalue(path3))
exp.design <- as.character(tclvalue(path4))
settings$tb6.var.shape.script <- as.character(tclvalue(tb6.var.shape.script))
tb6.var.shape.script <- as.character(tclvalue(tb6.var.shape.script))
if (tb6.var.shape.script=="1"){tb6.var.shape.script <- "TRUE"}else{tb6.var.shape.script = "FALSE"}
tb6.var.shape.script <- as.character(tb6.var.shape.script )
settings$tb5.var.p.adjust<- tclvalue(tb5.val.p.adjust)
tb5.val.p.adjust<- tclvalue(tb5.val.p.adjust)
settings$tb5.val.anova.p <- as.numeric(tclvalue(tb5.val.anova.p ))
tb5.val.anova.p <- as.numeric(tclvalue(tb5.val.anova.p ))
settings$tb5.var.do.go <- binary.rewrite(tb5.var.do.go)
settings$tb5.go.term.list <- tclvalue(tb5.val.go.term.list)
settings$tb5.val.volcano <- tclvalue(tb5.val.volcano)
settings$tb5.var.color.plots <- tclvalue(tb5.var.color.plots)
settings$tb5.var.graphic.type <- tclvalue(tb5.var.graphic.type)
settings$tb5.val.volcano <- tclvalue(tb5.val.volcano)
settings$tb5.do.cor <- tclvalue(tb5.val.do.cor)
settings$tb5.var.log2.ratio.thres <- tclvalue(tb5.var.log2.ratio.thres )
tb5.nb.2.fl.bp.frame.val.plot.type<- tclvalue(tb5.nb.2.fl.bp.frame.val.plot.type)
settings$tb5.nb.2.fl.bp.frame.val.plot.type <- tb5.nb.2.fl.bp.frame.val.plot.type
if(tb5.nb.2.fl.bp.frame.val.plot.type == tb5.1.2.fl.bp.frame.plot.type.var[1] ){
barpl = TRUE
time.grouped = FALSE
lineplot.beside = FALSE
}
if(tb5.nb.2.fl.bp.frame.val.plot.type == tb5.1.2.fl.bp.frame.plot.type.var[2] ){
barpl = TRUE
time.grouped = TRUE
lineplot.beside = FALSE
}
if(tb5.nb.2.fl.bp.frame.val.plot.type == tb5.1.2.fl.bp.frame.plot.type.var[3] ){
barpl = FALSE
time.grouped = FALSE
lineplot.beside = FALSE
}
if(tb5.nb.2.fl.bp.frame.val.plot.type == tb5.1.2.fl.bp.frame.plot.type.var[4] ){
barpl = FALSE
time.grouped = TRUE
lineplot.beside = FALSE
}
if(tb5.nb.2.fl.bp.frame.val.plot.type == tb5.1.2.fl.bp.frame.plot.type.var[5] ){
barpl = FALSE
time.grouped = TRUE
lineplot.beside = TRUE
}
settings$tb5.nb.2.fl.bp.frame.var.xlab <- tclvalue(tb5.1.2.fl.bp.frame.var.xlab)
settings$tb5.val.cluster.method <- tclvalue(tb5.val.cluster.method)
if(tclvalue(tb5.val.cluster.method) == "hclust"){
hclust.groups = TRUE}else{hclust.groups <- FALSE}
settings$tb5.val.anova.log2 <-tclvalue(tb5.val.anova.log2)
settings$val.onetailed.ttest <- tclvalue(tb5.val.onetailed.ttest)
####
# tb7
####
####
# rewrite settings
###
print("save settings")
try(
if(1==1&tclvalue(done) !=3){
tt2.settings.method <- as.character(tclvalue(tt2.settings.method))
if(tt2.settings.method == tt2.settings.var[1]){
try( save(settings,file= paste(path1.backup,"/settings.Rdata",sep ="")))
}
if(tt2.settings.method == tt2.settings.var[2]){}
if(tt2.settings.method == tt2.settings.var[3]){
load(paste(path1.backup,"/settings-standard.Rdata",sep =""))
try(save( settings,file = paste(path1.backup,"/settings.Rdata",sep ="")))
tclvalue(done) <- 4
}
})
print("saved settings")
#######
# returning list
#######
print(tclvalue(done))
if(tclvalue(done) == 2){ return(ReadAffy(
celfile.path = list(
settings = settings,
cracker = cracker,
path.data = path.data,
db = db.dat,
path.shape = path.script.shape,
msquant = tt2.experiment.name,
peptidenorm = tb1.val.replicates.cp,
raw = tb1.val.replicates,
peptidemerge = tb1.val.protein.intensity,
dupli.val = tb1.val.pep.duplicates,
ex.conrev = tb1.val.conrev,
use.raw = tab.4.var.raw.x,
norm.method = tclvalue(tb2.val.norm.method),
sum.of.total = sum.of.total,
score = tb2.val.score,
row.norm = tb2.var.rownorm,
shape = as.numeric(tclvalue(tb2.var.shape )),
expname = tt2.var.expname,
exclu = tb2.var.red.pep,
maxq.exclu = tb2.var.red.pep.mq,
group.norm = binary.rewrite(tb2.var.groupnorm),
group.filter = binary.rewrite(tb2.var.group.filternorm),
outlier = tb3.var.outlier,
phospho = tb3.var.phospho,
phospho.protein = tb3.var.phospho.protein,
zero.treat = tb3.val.zero.treat,
build.matrix = TRUE,#tb3.var.build.matrix,
#plot.only = binary.rewrite(tb3.var.plot.only),
plot.only = tclvalue(path5),
cbn.prot = tb4.val.cbn.prot,
shape.prot.norm = as.numeric(tclvalue(tb4.val.cbn.shape)),
n.correction = n.correction,
#position = tkwm.geometry(tb1)
N15 = tb4.val.n15,
row.target.norm = tb4.var2.cbn,
n15.log2 = tb4.val.n15.log ,
n15.correct.method = tb4.val.n15.log.correction,
n15.correct.expect = tb4.val.ratio,
centers = tb5.val.kmeans,
p.adjust.method = tb5.val.p.adjust,
p.value = tb5.val.anova.p,
log2.test = binary.rewrite(tb5.val.anova.log2),
volcano = binary.rewrite(tb5.val.volcano),
onetailed.ttest = binary.rewrite(tb5.val.onetailed.ttest),
graphic.type = tclvalue(tb5.var.graphic.type),
ratio.thres = tclvalue(tb5.var.log2.ratio.thres),
do.GO = binary.rewrite(tb5.var.do.go),#tb5.do.go.m
go.library = paste("cRackerMapping-",tclvalue(tb5.val.go.term.list),sep = ""),
do.cor = tclvalue(tb5.val.do.cor),
do.network = binary.rewrite(tb5.var.do.network),
color.plots = tclvalue(tb5.var.color.plots),
barpl = barpl,
time.grouped = time.grouped,
lineplot.beside = lineplot.beside,
x.xlab = as.character(tclvalue(tb5.1.2.fl.bp.frame.var.xlab)),
exp.design = exp.design,
hclust.groups = hclust.groups,
script.shape = tb6.var.shape.script ,
quant.method = tb4.quant.method,
calc.empai = FALSE,
empai.sd = FALSE,
empai.from.msms = FALSE,
empai.pep.length= 6,
empai.reference = ""
)))}else{
if(tclvalue(done) == 3){return("switch")}
if(tclvalue(done) == 1){return("stopped")}
if(tclvalue(done) == 4){return("reload")}
}
}
#print(gui.input<- hz.read.parameters(path1 =("/Users/henno/cracker/pkg/data/"),path2 = "",path2.set = list(settings = "",2,3),.data = ""))
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