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inst/shiny-examples/DOSCHEDA_app/app.R
In Doscheda: A DownStream Chemo-Proteomics Analysis Pipeline
# https://bruniec.shinyapps.io/doscheda/
library(hexbin)
library(MASS)
library(shiny)
library(shinydashboard)
library(stringr)
library(affy)
library(limma)
library(DT)
library(ggplot2)
library(vsn)
library(gridExtra)
library(lattice)
library(corrgram)
library(calibrate)
library(reshape2)
library(readxl)
library(MASS)
library(lazyeval)
library(drc)
library(httr)
library(jsonlite)
library(rmarkdown)
library(dplyr)
library(prodlim)
################### Load Function
loadingLogo <- function( src, loadingsrc, height = NULL, width = NULL, alt = NULL) {
tagList(
tags$head(
tags$script(
"setInterval(function(){
if ($('html').attr('class')=='shiny-busy') {
$('div.busy').show();
$('div.notbusy').hide();
} else {
$('div.busy').hide();
$('div.notbusy').show();
}
},100)")
),
tags$a(
div(class = "busy",
img(src=loadingsrc,height = height, width = width, alt = alt)),
div(class = 'notbusy',
img(src = src, height = height, width = width, alt = alt))
)
)
}
# plotting functions for sigmoidal
shape_for_ggplot_pred<-function(df_ordered,conc,pred.names){
cols_to_keep_pred<-c(pred.names,"GeneID","Accession")
forggplot_pred<-vector(mode = "list",length = length(df_ordered$GeneID))
for(i in 1:length(df_ordered$GeneID)){
tmp_pred<-df_ordered[,cols_to_keep_pred]
forggplot_pred[[i]]<-melt(tmp_pred[i,], id = c("GeneID", "Accession"), na.rm = TRUE)
}
forggplot_pred_1<-do.call(rbind, forggplot_pred)
forggplot_pred_1<-data.frame(forggplot_pred_1,"x"=conc)
#return(forggplot_pred_1)
}
shape_for_ggplot_perc<-function(df_ordered,conc,finalNames){
cols_to_keep_perc<-c(finalNames, "GeneID","Accession")
forggplot_perc<- vector(mode = "list",length = length(df_ordered$GeneID))
for(i in 1:length(df_ordered$GeneID)){
tmp_perc<-df_ordered[,cols_to_keep_perc]
forggplot_perc[[i]]<-melt(tmp_perc[i,], id = c("GeneID", "Accession"), na.rm = TRUE)
}
forggplot_perc_1<-do.call(rbind, forggplot_perc)
forggplot_perc_1<-data.frame(forggplot_perc_1,"x"=conc)
#return(forggplot_perc_1)
}
pie_chart <- function(df, main, labels = NULL, condition = NULL) {
# convert the data into percentages. group by conditional variable if needed
df <- group_by_(df, .dots = c(condition, main)) %>%
summarise(counts = n()) %>%
mutate(perc = counts / sum(counts)) %>%
arrange(desc(perc)) %>%
mutate(label_pos = cumsum(perc) - perc / 2,
perc_text = paste0(round(perc * 100), "%", "\n","(",counts, ")"))
# reorder the category factor levels to order the legend
df[[main]] <- factor(df[[main]], levels = unique(df[[main]]))
# if labels haven't been specified, use what's already there
if (is.null(labels)) labels <- as.character(df[[main]])
p <- ggplot(data = df, aes_string(x = factor(1), y = "perc", fill = main)) +
# make stacked bar chart with black border
geom_bar(stat = "identity", color = "black", width = 1) +
# add the percents to the interior of the chart
geom_text(aes(x = 1.25, y = label_pos, label = perc_text), size = 4) +
# add the category labels to the chart
# increase x / play with label strings if labels aren't pretty
geom_text(aes(x = 1.82, y = label_pos, label = labels), size = 4) +
# convert to polar coordinates
coord_polar(theta = "y") +
# formatting
scale_y_continuous(breaks = NULL) +
scale_fill_discrete(name = "", labels = unique(labels)) +
theme(text = element_text(size = 12),
axis.ticks = element_blank(),
axis.text = element_blank(),
axis.title = element_blank())
# facet wrap if that's happening
if (!is.null(condition)) p <- p + facet_wrap(condition)
return(p)
}
##upload kinase file
kinome1<-read.csv(file="KinaseFile.csv", header=TRUE, sep=",")
kinome<-as.vector(toupper(kinome1$new.Symbol))
logvc<- function(x) sqrt(exp(x*log(2))^2 - 1 )
# Peptide matching function
peptide.match<- function(dr1,dr2,nchan){
maxrow <- max(nrow(dr1),nrow(dr2))
minrow <- min(nrow(dr1),nrow(dr2))
adVal <- maxrow - minrow
if(nrow(dr1) == maxrow){
dr2$addedVals <- adVal
big.pep <- dr1
small.pep <- dr2
} else {
dr1$addedVals <- adVal
big.pep <- dr2
small.pep <- dr1
}
newframe <- big.pep
colnames(newframe) <- colnames(small.pep)
newframe[1:minrow,] <- small.pep
for(i in 1:nchan){
newframe[(minrow+1):maxrow,i]<- mean(small.pep[,i])
}
if (all.equal(dim(big.pep),dim(dr1)) == TRUE){
dr2 <- newframe
} else {
dr1 <- newframe
}
list(dr1 = dr1, dr2 = dr2 )
}
panel.shadeNtext <- function (x, y, corr = NULL, col.regions, ...)
{
if (is.null(corr))
corr <- cor(x, y, use = "
pair")
ncol <- 14
pal <- col.regions(ncol)
col.ind <- as.numeric(cut(corr, breaks = seq(from = -1, to = 1,
length = ncol + 1), include.lowest = TRUE))
usr <- par("usr")
rect(usr[1], usr[3], usr[2], usr[4], col = pal[col.ind],
border = NA)
box(col = "lightgray")
on.exit(par(usr))
par(usr = c(0, 1, 0, 1))
r <- formatC(corr, digits = 2, format = "f")
cex.cor <- .8/strwidth("-X.xx")
text(0.5, 0.5, r, cex = cex.cor)
}
#########################################################################
## UI
#########################################################################
ui <- shinyUI(dashboardPage(
dashboardHeader(title = loadingLogo('titleogo.png','logogifopt.gif',height = 55,width = 165)),
dashboardSidebar(
sidebarMenu(id = "menu1",
menuItem(text = "Introduction", tabName = "intro"),
#menuItem(text = "Step by Step Guide", tabName = 'stbyst'),
conditionalPanel(
condition = "input.menu1 == 'stbyst'",
radioButtons(inputId = "stage",label = NULL, choices =
c("Stage 1: Data Upload" = "stage1",
"Stage 2: Navigating Plots" = "stage2",
"Stage 3: Download Results" = "stage3"))
),
menuItem(text = "Data Upload", tabName = "dataload"),
menuItem(text = "Box and Density Plots", tabName = "box"),
menuItem(text = "MeanSD Plot", tabName = "meansd"),
menuItem(text = "Mean vs Difference", tabName = "meandiff"),
conditionalPanel(
condition = "input.menu1 == 'meandiff'",
uiOutput("meandiff1")
),
menuItem(text = "Corrgram",tabName = "corrgram"),
menuItem(text = "Compare Replicates",tabName = "repvsrep"),
conditionalPanel(
condition = "input.menu1 == 'repvsrep'",
uiOutput("repvsrep1") ),
menuItem(text = "PCA", tabName = "pca"),
menuItem(text = "Heatmap", tabName = "testsigmoid"),
menuItem(text = "Linear Model", tabName = "volcano"),
conditionalPanel(
condition = "input.menu1 == 'volcano' & input.modtyp == 'lin'",
sliderInput(inputId = "pvalsli", label = "Change Pvalue threshold",min = 0,max = 0.1,value = 0.05),
sliderInput(inputId = "avthrssli", label = "Change avfold threshold",min = 0,max = 1,value = 0.2)
),
menuItem(text = "Sigmoidal fit",tabName = "sigfit"),
menuItem(text = "Summary", tabName = "summary"),
menuItem(text = "Download", tabName = "download"),
menuItem(text = "Session Log", tabName = "tst")
)
),
dashboardBody(
tabItems(
tabItem(tabName = 'tst',box(htmlOutput("sessionInfo"),width = 12)),
tabItem(tabName = "testsigmoid",
box(width = 12, height = 800,
plotOutput("plot9",height = 750)
)),
tabItem(tabName = "intro", includeHTML(path ="introduction.html")),
# The step by step has been removed from the app but can be re instated by including the menuItem at the start of the UI
tabItem(tabName = "stbyst",
conditionalPanel(condition = 'input.stage == "stage1"',
tabBox(id = 'stg1tabs', width = 12,
tabPanel(title = "Step 1",
h4("Go to the tab on the sidebar"),
br(),br()
,HTML('<p><img src="stage1step1.gif" height = 500 /></p>')
),
tabPanel(title = "Step 2",
h4("Select your data type, please note that intensities will take a few minutes to run."),
br(),HTML('<p><img src="stage1step2.gif" height = 450 /></p>')
),
tabPanel(title = "Step 3",
h4("Select the number of channels and replicates."),
br(),
HTML('<p><img src="stage1step3.gif" height = 450 /></p>')
),
tabPanel(title = "Step 4",
h4("Choose the columns from your data set which indicate the channels you would like to analyse. Note that you can search for these column names by typing in the input box."),
br(),h4("Remember to check that the uploaded column names correspond with the correct standardised name by looking at the table. You can change these positions by dragging and dropping the selected column names in the desired order in the input box."),
br(),HTML('<p><img src="stage1step4.gif" height = 450 /></p>')
),
tabPanel(title = "Step 5",
h4("(optional depending on input) If you would like to apply a sigmoidal fit and have an adequate amount of data, use the radio button to change the fit and input your concentrations, separating them with a comma
. Please Note that this may take a few minutes to run"),
br(),HTML('<p><img src="doschedasigmoid.gif" height = 450 /></p>')
),
tabPanel(title = "Step 6",
h4("(optional depending on input) If you are using intensities, you required to input the peptide quality score and sequence."),
br(),HTML('<p><img src="doschedaintensity.gif" height = 450 /></p>')),
tabPanel(title = "Step 7",
h4("Change to one of the plot tabs and you will see the loading sign appear in place of the logo, now cycle through all the tabs.")
)
)),
conditionalPanel(condition = 'input.stage == "stage2"'
,
tabBox(id = 'stg2tabs', width = 12,
tabPanel(title = "Stage 2",
h4(" Cycle through plots, this is done by clicking on the sidebar tabs and the tabs within the main panel.")
))
),
conditionalPanel(condition = 'input.stage == "stage3"'
,
tabBox(id = 'stg3tabs', width = 12,
tabPanel(title = "Download Data",
h4("Go to the Download tab and press the Download Data button to download the processed data in csv format. and use the ‘Download Report’ to download a html file with all your plots with descriptions with them to save your results from the pipeline.")
),
tabPanel(title = "Download Report",
h4("Go to the Download tab and press the ‘Download Report’ button to download a html file with all your plots with description, allowing you to save your results from the pipeline.")
)
)
)),
# End of the step by step
tabItem(tabName = "dataload",
box(width = 4,
fluidRow(column(5,radioButtons("datype", "Data Type:",
c("Intensities" = "intensity",
"Fold Change" = "FC",
"Log-Fold Change" = "lFC"))),
column(5,radioButtons("filetype", "File Type:",
c(".csv" = "CSV",
".txt" = "TXT",
".xlsx" = "XLSX")))
),
conditionalPanel(condition = 'input.datype == "intensity" & input.modtyp != "sigmoid"',
radioButtons("dorem", "Do removal:",
c("Yes" = "yes",
"No" = "no"),selected = 'no')
)
,
# DATA file upload
fileInput('file2', 'Choose file',
accept = c(".txt",".csv",".xlsx")),
fluidRow(column(5, numericInput("chans","# Channels",value = 4, min = 1)),
column(5, numericInput("reps","# Replicates",value = 1,min = 1))
),
actionButton("changenames", label = "Change Names"),
conditionalPanel(condition = "(input.changenames % 2) == 1",
uiOutput("setNames")
),
uiOutput("ui_choice"),
radioButtons(inputId = "normalize",label = 'Choose Normalization', choices =
c("LOESS" = "loess",
"Median" = "median",
"None" = "none"),
selected = 'loess'
),
conditionalPanel(condition = 'input.datype == "intensity"',
uiOutput("ui_sequence"),
uiOutput("ui_qual"),
numericInput('pearsvar',label = "Pearson Variable", value = 0.4,min = -1,max = 1,step = 0.1)
),
conditionalPanel(condition = 'input.toacc == true || input.datype == "intensity"',
uiOutput("ui_accession")
),
conditionalPanel(condition = 'input.toacc == true & input.datype != "intensity"',
uiOutput("ui_uniqpep")
),
conditionalPanel(condition = "input.modtyp == 'sigmoid'",
checkboxInput('incpd', 'Insert pulldown of pull down', value = FALSE)
),
conditionalPanel(condition = 'input.incpd == true',
uiOutput("ui_pdofpd")
),
conditionalPanel( condition = "input.datype != 'intensity'",
checkboxInput("toacc", "Data is NOT Proteome Discoverer 2.1", FALSE)
),
checkboxInput('genefile', 'Upload an Accession to Gene ID file', value = FALSE)
# uiOutput("ui_sequence"),
## remove column obselete
# fluidRow(
# column(5,conditionalPanel(
# condition = "input.conf != 0",
# actionButton(inputId = "removechan", label = "Remove Column")
# ))),
#
# conditionalPanel(
# condition = "(input.removechan % 2) == 1",
# uiOutput("remchan")
# )
),
box(width = 8,
DT::dataTableOutput("test")
),
box(width = 8,
conditionalPanel(condition = 'input.chans >= 5 & input.reps == 1',
radioButtons("modtyp", "Fit model:",
c("Sigmoidal" = "sigmoid",
"Linear" = "lin"
),selected = "lin")),
conditionalPanel(condition = 'input.chans < 5',
h1("Less than 5 channels, only a linear model can be applied")
),
conditionalPanel(condition = "input.modtyp == 'sigmoid'",
textInput("concsig", "Enter vector of concentrations from low to high [comma delimited]. Ensure these are not log concentrations"),
textOutput("concsig")
)
),
box(width = 8,
selectizeInput( 'organism',label = 'Select your organism:', choice = c('H.sapiens','C. familiaris','D.melanogaster','M. musculus','R. norvegicus', 'S.cerevisiae'), selected = 'H.sapiens'),
conditionalPanel(condition = 'input.genefile == true',
fluidRow(column(5,fileInput('geneF', 'Choose you Accession to Gene ID file',
accept = c(".txt",".csv",".xlsx"))),
column(5,radioButtons("generadio", "File Type:",
c(".csv" = "CSV",
".txt" = "TXT",
".xlsx" = "XLSX"))
))
)
)
),
tabItem(tabName = "box",
fluidRow(
tabBox(id = "tb1", width = 9, height = 700,
tabPanel("Box",plotOutput(height = 700, "bar")),
tabPanel("Density", plotOutput(height = 700, "plot2")),
tabPanel("Venn", plotOutput(height = 700, "venn"))
),
box(width = 3,
conditionalPanel(condition = "input.tb1 == 'Venn'",
checkboxInput(inputId = 'venninput' ,label = 'Include file', value = FALSE)
),
conditionalPanel('input.venninput == true',
radioButtons("filetype2", "File Type:",
c(".csv" = "CSV",
".txt" = "TXT",
".xlsx" = "XLSX")),
fileInput(inputId = 'venninp',label = 'Choose input file',
accept = c(".txt",".csv",".xlsx") )
)
)
)
),
tabItem(tabName = "meansd",
fluidRow(box(width = 9, height = 700, plotOutput(height = 600, "plot3")))),
tabItem(tabName = "meandiff",
fluidRow(
box(width = 9, height = 700, plotOutput(height = 600, "plot6"))
)),
tabItem("corrgram", fluidRow(box(width = 9, height = 800, plotOutput(height = 700,"plot5")))
),
tabItem("repvsrep", fluidRow(box(width = 9, height = 800, plotOutput(height = 700,"repvsrep")))),
tabItem(tabName = "pca", fluidRow( box(width = 9, height = 800, plotOutput(height = 700,"plot7")))),
tabItem(tabName = "volcano", fluidRow( tabBox(id = "volplots", width = 9, height = 800,
tabPanel(title = "P-Value Distribution",plotOutput(height = 700,"plot4")),
tabPanel(title = "Slope", plotOutput(height = 700,"plot8")),
tabPanel(title = "Intercept", plotOutput(height = 700,"volcanoint")),
tabPanel(title = "Quadratic", plotOutput(height = 700,"volcanoquad"))
))),
tabItem(tabName = "sigfit", fluidRow( tabBox(id = "sigplots", width = 10, height = 800,
tabPanel(title = "Difference Top-Bottom",plotOutput(height = 700,"DiffTopBottom")),
tabPanel(title = "RB50", plotOutput(height = 700,"RB50")),
tabPanel(title = "Slope", plotOutput(height = 700,"Slope_pl"))
))),
tabItem(tabName = "summary", fluidRow(
tabBox(id = "sumtab", width = 8,
tabPanel("Data p-values",div(DT::dataTableOutput("testmerge",width = '100%'),style = "font-size:90%")),
tabPanel("Kinases", DT::dataTableOutput("kintab"))
),box(title = "Corrgram QC", width = 4,
infoBoxOutput(outputId = "corrinfo",width = 12)
),box(title = "P Value QC", width = 4,
conditionalPanel(condition = "input.modtyp == 'sigmoid'",
infoBoxOutput("siginfodt",width = 12),
infoBoxOutput("siginfoslop",width = 12),
infoBoxOutput("siginfodiff",width = 12)
),
conditionalPanel(condition = "input.modtyp != 'sigmoid'",
infoBoxOutput(outputId = "infopvalslo",width = 12),
br(),br(),br(), br(),br(), br(),
infoBoxOutput(outputId = "infopvalint",width = 12),
br(),br(),br(), br(),br(), br(),
infoBoxOutput(outputId = "infopvalquad",width = 12)
)
)
)),
tabItem(tabName = "download",
box(width = 12,
textInput("dataset", "Filename for Data", value = "Doscheda"),
downloadButton('downloadData', 'Download Data'),
downloadButton("report", "Generate report")
),
box(width = 12,
conditionalPanel(condition = "input.datype == 'intensity'",
actionButton(inputId = 'intcalc',"Calculate Removed Peptides")
), br(),
conditionalPanel(condition = "input.intcalc != 0",
downloadButton('peprmv', "Download Removed Peptides")
)
)
)
)
)
))
#########################################################
## SERVER
#########################################################
server <- shinyServer(function(input, output) {
options(shiny.maxRequestSize=100*1024^2)
##############################################
## uniprot gene load in any changes to uni prot file will affect this section
uniprotGene <- reactive({
if(input$organism == 'H.sapiens'){
query = '<query model="genomic" view="Protein.primaryAccession Protein.uniprotAccession Protein.genes.symbol" sortOrder="Protein.primaryAccession ASC" >
<constraint path="Protein.organism.shortName" op="=" value="H. sapiens" code="A" />
</query>'
ret=POST('http://www.humanmine.org/humanmine/service/query/results',
body=list(query=query, format='json'),
encode='form')
} else if(input$organism == 'D. melanogaster'){
query = '<query model="genomic" view="Protein.primaryAccession Protein.uniprotAccession Protein.genes.symbol" sortOrder="Protein.primaryAccession ASC" >
<constraint path="Protein.organism.shortName" op="=" value="D. melanogaster" code="A" />
</query>'
ret=POST('http://www.flymine.org/flymine/service/query/results',
body=list(query=query, format='json'),
encode='form')
}else if(input$organism == 'M. musculus'){
query = '<query model="genomic" view="Protein.primaryAccession Protein.uniprotAccession Protein.genes.symbol" sortOrder="Protein.primaryAccession ASC" >
<constraint path="Protein.organism.shortName" op="=" value="M. musculus" code="A" />
</query>'
ret = POST('http://www.mousemine.org/mousemine/service/query/results',
body=list(query=query, format='json'),
encode='form')
}else if (input$organism == 'R. norvegicus'){
query = '<query model="genomic" view="Protein.primaryAccession Protein.uniprotAccession Protein.genes.symbol" sortOrder="Protein.primaryAccession ASC" >
<constraint path="Protein.organism.shortName" op="=" value="R. norvegicus" code="A" />
</query>'
ret = POST('http://www.ratmine.org/ratmine/service/query/results',
body=list(query=query, format='json'),
encode='form')
}else{
query = '<query model="genomic" view="Protein.primaryAccession Protein.uniprotAccession Protein.genes.symbol" sortOrder="Protein.primaryAccession ASC" >
<constraint path="Protein.organism.shortName" op="=" value="C. elegans" code="A" />
</query>'
ret=POST('http://www.humanmine.org/humanmine/service/query/results',
body=list(query=query, format='json'),
encode='form')
}
response = jsonlite::fromJSON(httr::content(ret,as='text'))
data.prots <- response$results[,c(1,3)]
colnames(data.prots) <- c('Entry','Gene.names')
as.data.frame(data.prots[,1:2],stringsAsFactors = FALSE)
})
## upload gene file
uploadGene <- reactive({
inFile <- input$geneF
if(is.null(inFile)){
return(NULL)
}
if( input$generadio == "TXT"){
file.rename(inFile$datapath,
paste(inFile$datapath, ".txt", sep=""))
# read.xlsx(paste(inFile$datapath, ".xlsx", sep=""),
# sheetIndex = 1, header = TRUE, stringsAsFactors = FALSE)
conv<- read.delim(paste(inFile$datapath, ".txt", sep=""),
header = TRUE,stringsAsFactors = FALSE)
} else if (input$generadio == "XLSX"){
file.rename(inFile$datapath,
paste(inFile$datapath, ".xlsx", sep=""))
# paste(inFile$datapath, ".xlsx", sep=""))
# read.xlsx(paste(inFile$datapath, ".xlsx", sep=""),
# sheetIndex = 1, header = TRUE, stringsAsFactors = FALSE)
conv<- read_excel(paste(inFile$datapath, ".xlsx", sep=""),
sheet = 1)
} else {
file.rename(inFile$datapath,
paste(inFile$datapath, ".csv", sep=""))
# paste(inFile$datapath, ".xlsx", sep=""))
# read.xlsx(paste(inFile$datapath, ".xlsx", sep=""),
# sheetIndex = 1, header = TRUE, stringsAsFactors = FALSE)
conv<- read.csv(paste(inFile$datapath, ".csv", sep=""), header = TRUE, stringsAsFactors = FALSE)
conv<- conv[,-1]
}
conv <- conv[,1:2]
colnames(conv) <- c('Entry', 'Gene.names')
conv
})
## venn diagram intersect file upload
uploadVenn <- reactive({
if(input$venninput == FALSE){
return(NULL)
} else{
inFile <- input$venninp
if(is.null(inFile)){
return(NULL)
}
if( input$filetype2 == "TXT"){
file.rename(inFile$datapath,
paste(inFile$datapath, ".txt", sep=""))
# read.xlsx(paste(inFile$datapath, ".xlsx", sep=""),
# sheetIndex = 1, header = TRUE, stringsAsFactors = FALSE)
conv<- read.delim(paste(inFile$datapath, ".txt", sep=""),
header = TRUE,stringsAsFactors = FALSE)
} else if (input$filetype2 == "XLSX"){
file.rename(inFile$datapath,
paste(inFile$datapath, ".xlsx", sep=""))
# paste(inFile$datapath, ".xlsx", sep=""))
# read.xlsx(paste(inFile$datapath, ".xlsx", sep=""),
# sheetIndex = 1, header = TRUE, stringsAsFactors = FALSE)
conv<- read_excel(paste(inFile$datapath, ".xlsx", sep=""),
sheet = 1)
} else {
file.rename(inFile$datapath,
paste(inFile$datapath, ".csv", sep=""))
# paste(inFile$datapath, ".xlsx", sep=""))
# read.xlsx(paste(inFile$datapath, ".xlsx", sep=""),
# sheetIndex = 1, header = TRUE, stringsAsFactors = FALSE)
conv<- read.csv(paste(inFile$datapath, ".csv", sep=""), header = TRUE, stringsAsFactors = FALSE)
conv<- conv[,-1]
}
conv
}
})
### crapome file upload
crapome<- reactive({
if(input$organism == 'S.cerevisiae'){
a <- read.csv('CRAPOME_YEAST',stringsAsFactors = FALSE)
} else{
a <- read.csv('CRAPOME_HUMAN',stringsAsFactors = FALSE)
}
print(head(a))
a
})
### DATA file upload
data <- reactive({
inFile <- input$file2
if(is.null(inFile)){
return(NULL)
}
if( input$filetype == "TXT"){
file.rename(inFile$datapath,
paste(inFile$datapath, ".txt", sep=""))
# read.xlsx(paste(inFile$datapath, ".xlsx", sep=""),
# sheetIndex = 1, header = TRUE, stringsAsFactors = FALSE)
conv<- read.delim(paste(inFile$datapath, ".txt", sep=""),
header = TRUE,stringsAsFactors = FALSE)
} else if (input$filetype == "XLSX"){
file.rename(inFile$datapath,
paste(inFile$datapath, ".xlsx", sep=""))
# paste(inFile$datapath, ".xlsx", sep=""))
# read.xlsx(paste(inFile$datapath, ".xlsx", sep=""),
# sheetIndex = 1, header = TRUE, stringsAsFactors = FALSE)
conv<- read_excel(paste(inFile$datapath, ".xlsx", sep=""),
sheet = 1)
} else {
file.rename(inFile$datapath,
paste(inFile$datapath, ".csv", sep=""))
# paste(inFile$datapath, ".xlsx", sep=""))
# read.xlsx(paste(inFile$datapath, ".xlsx", sep=""),
# sheetIndex = 1, header = TRUE, stringsAsFactors = FALSE)
conv<- read.csv(paste(inFile$datapath, ".csv", sep=""), header = TRUE, stringsAsFactors = FALSE)
}
data.frame(conv)
})
## ui elements
output$ui_accession<- renderUI({
temp <- data()
## using selectizeInput with drag_drop and DT
selectizeInput("accession", "Choose Accession", choices = colnames(temp) ,
selected = NULL,
multiple = FALSE,
options = list(plugins = list('remove_button')))
})
output$ui_uniqpep<- renderUI({
temp <- data()
## using selectizeInput with drag_drop and DT
selectizeInput("unipeps", "Choose Unique Peptides", choices = colnames(temp) ,
selected = NULL,
multiple = FALSE,
options = list(plugins = list('remove_button')))
})
output$ui_pdofpd<- renderUI({
temp <- data()
## using selectizeInput with drag_drop and DT
selectizeInput("pdofpd", "Choose Pulldown of pulldown", choices = colnames(temp) ,
selected = NULL,
multiple = FALSE,
options = list(plugins = list('remove_button')))
})
output$ui_sequence<- renderUI({
temp <- data()
## using selectizeInput with drag_drop and DT
selectizeInput("sequence", "Choose Sequence", choices = colnames(temp) ,
selected = NULL,
multiple = FALSE,
options = list(plugins = list('remove_button')))
})
output$ui_choice<- renderUI({
reqtemp <- data()
req(reqtemp)
## using selectizeInput with drag_drop and DT
selectizeInput("view_vars", "Select variables to show:", choices = colNamTot(),
selected = colNamSel(),
multiple = TRUE,
options = list(plugins = list('remove_button', 'drag_drop'), maxItems = nchans()))
})
output$ui_qual<- renderUI({
reqtemp <- data()
req(reqtemp)
## using selectizeInput with drag_drop and DT
selectizeInput("quality", "Select Peptide Qvality Score:", choices = colNamTot(),
selected = colNamSel(),
multiple = FALSE,
options = list(plugins = list('remove_button', 'drag_drop'), maxItems = 1))
})
output$remchan<- renderUI({
reqtemp <- data()
req(reqtemp)
selectizeInput(
'remchan', 'Choose Channels to remove', choices = finalNames(), multiple = TRUE,
options = list(plugins = list('remove_button'))
)
})
## final names setting
standardNames <- reactive({
if(input$datype == "intensity"){
out<- paste("rep",rep(1:input$reps,each = input$chans),"_",
rep(paste("C",c("ontrol",0:(input$chans - 2)), sep = ""),input$reps),sep = "")
vals$labelNames = setNames(out, out)
}else{
out<- paste("rep",rep(1:input$reps,each = input$chans),"_",
rep(paste("C",0:(input$chans - 1), sep = ""),input$reps),sep = "")
vals$labelNames = setNames(out, out)
}
return(out)
})
output$setNames <- renderUI({
list(
h4("Change Names")
, selectInput("nameToChange", "Standard name"
, names(vals$labelNames))
, textInput("labelToAdd", "Change to")
, actionButton("makeLabel", "Set label")
)
})
observeEvent(input$makeLabel, {
vals$labelNames[input$nameToChange] <- input$labelToAdd
})
finalNames<- reactive({
vals$labelNames
})
##############################################
sigConc <- reactive({
if(input$modtyp == "sigmoid"){
sort(as.numeric(unlist(strsplit(input$concsig,","))))
}else{
return(NULL)
}
})
output$concsig <- renderText({
x <- as.numeric(unlist(strsplit(input$concsig,",")))
if(input$datype== 'intensity'){
n<- input$chans - 1
}else{
n <- input$chans*input$reps
}
if(length(x) < n){
paste0("Not enough concentrations, please put ",n," concentrations")
} else if(length(x) > n){
paste0("Too many concentrations, please put ",n," concentrations")
}else{
x<- sort(x)
print(c("Concentrations:",x))
}
})
output$selectnames <- renderUI({
selectizeInput("selectnames", "Change Names", choices = standardNames(),
options = list(maxOptions = input$reps * input$chans))
})
vals <- reactiveValues(
labelNames = character()
)
#### LABEL UPLOAD
#### data imported and finalNames is vector of colnames ####
rReps <- reactive({
input$reps
})
nchans <- reactive({
input$reps * input$chans
})
### probably dont need this
### datachange table
### selectize
colNamTot<- reactive({
reqtemp <- data()
req(reqtemp)
a2 <- data()
colnames(a2)
})
colNamSel<- reactive({
a1 <- data()
a1 <- colnames(a1)
sample(a1,nchans())
})
indexmatrix <- reactive({
reqtemp <- data()
req(reqtemp)
if(input$reps <= 1){
NULL
} else {
if(input$datype == "intensity"){
channe <- channels()
reps <- input$reps
chans <- input$chans - 1
ser <- finalNames()
ser<- ser[-seq(1,by = input$chans,length.out = input$reps)]
}else{
ser <- finalNames()
channe <- channels()
reps <- input$reps
chans <- input$chans
}
combinations <- t(combn(reps,2))
combmat<- matrix(rep(as.vector(t(combinations)),chans),ncol = 2,byrow = TRUE)
# create factor for repeat ...
name.vec <- 1:(chans*reps)
repfac <- rep(1:chans,times = reps)
index <- rep(0:(reps-1),each = chans)
combfac<- rep(1:(reps),each = chans)
# total combinations = chans * nrow()
columnindex <- matrix(0 , ncol = 5 , nrow = chans * nrow(combinations) )
colnames(columnindex) <- c("concentration","rep1","rep2","index1","index2")
columnindex[,1] <- rep(1:chans ,each = nrow(combinations))
columnindex[,2:3]<- combmat
columnindex
# create matrix which will be indexed by first 3 columns of column index
index.mat <- matrix(name.vec,ncol = reps)
for(i in 1:nrow(columnindex)){
columnindex[i,4] <- index.mat[columnindex[i,1],columnindex[i,2]]
columnindex[i,5] <- index.mat[columnindex[i,1],columnindex[i,3]]
}
dadt <- dataMerge()
create.names <- rep("", nrow(columnindex))
for( i in 1:nrow(columnindex)){
create.names[i] <- paste(ser[columnindex[i,4]], "vs", ser[columnindex[i,5]])
}
final.mat <- data.frame(names = create.names,columnindex)
final.mat
final.mat[!is.na(rowSums(matrix(match(columnindex,channe),ncol=5))),]
}
})
selRemCol <- reactive({
reqtemp <- data()
req(reqtemp)
a1<- finalNames()
a1<- as.character(a1)
if(is.null(input$remchan)){
0
}else{
-match(input$remchan,a1)
}
})
channels <- reactive({
reqtemp <- data()
req(reqtemp)
if(input$datype == 'intensity'){
if(input$reps == 1){
1:(input$chans*input$reps -1)
}else{
1:(input$chans*input$reps -2)
}
}else{
a1 <- selRemCol()
vec <- 1:nchans()
if(a1 != 0){
vec <- vec[selRemCol()]
}
vec
}
})
##### DATA HANDLING #####
## Intensities
intData <- reactive({
if(input$datype == "intensity"){
tempdat <- data()
# make matrix of descriptions and accessions to filter by common proteins
accDesMat<- as.character(tempdat[as.character(tempdat[,input$accession]) == "",c(input$accession)])
if(input$incpd == TRUE){
data.merged <- tempdat[,c(input$view_vars, input$accession, input$sequence,input$quality,input$pdofpd)]
}else{
data.merged <- tempdat[,c(input$view_vars, input$accession, input$sequence,input$quality)]
}
channelnames <- standardNames()
repindex <- rep(1:input$reps,each = input$chans)
totfal <- rep(FALSE , (input$chans + 3 ))
if(input$incpd == TRUE){
newdf <- cbind(data.merged[,1:input$chans], data.merged[,c(input$accession, input$sequence,input$quality,input$pdofpd)])
colnames(newdf) <- c(channelnames[repindex == 1],"Accession","Sequence", "Quality",'Kd')
newdf <- newdf[!is.na(rowSums(newdf[,1:input$chans])),]
newdf <- newdf[newdf$Quality <= 0.05, ]
newdf <- data.frame(newdf, outliers = rep(0,length(newdf[,1])), uniquePeps = rep(0,length(newdf[,1])), addedVals = rep(0,length(newdf[,1])),Kd = newdf$Kd)
}else{
newdf <- cbind(data.merged[,1:input$chans], data.merged[,c(input$accession, input$sequence,input$quality)])
colnames(newdf) <- c(channelnames[repindex == 1],"Accession","Sequence", "Quality")
newdf <- newdf[!is.na(rowSums(newdf[,1:input$chans])),]
newdf <- newdf[newdf$Quality <= 0.05, ]
}
if(input$reps == 2){
channelnames <- paste("rep",rep(1:input$reps,each = input$chans),"_",
rep(paste("C",c("ontrol",0:(input$chans - 2)), sep = ""),input$reps),sep = "")
newdf2 <- cbind(data.merged[,(input$chans+1):(2*input$chans) ],data.merged[,c(input$accession, input$sequence,input$quality)])
colnames(newdf2) <- c(channelnames[repindex == 2],"Accession","Sequence","Quality")
newdf2 <- newdf2[!is.na(rowSums(newdf2[,1:input$chans])),]
newdf2 <- newdf2[newdf2$Quality <= 0.05, ]
newdf <- data.frame(newdf, outliers = rep(0,length(newdf[,1])), uniquePeps = rep(0,length(newdf[,1])), addedVals = rep(0,length(newdf[,1])))
newdf2 <- data.frame(newdf2, outliers = rep(0,length(newdf2[,1])), uniquePeps = rep(0,length(newdf2[,1])), addedVals = rep(0,length(newdf2[,1])))
common.proteins <- intersect(unique(newdf$Accession),unique(newdf2$Accession))
newdf <- newdf[!is.na(match(newdf$Accession,common.proteins)),]
newdf2 <- newdf2[!is.na(match(newdf2$Accession,common.proteins)),]
}else{
common.proteins <- unique(newdf$Accession)
}
if(input$dorem == "no"){
if(input$reps == 1){
if(input$incpd == TRUE){
prot1 <- unique(newdf$Accession)
sumkd <- rep(0,length(prot1))
protdf<- newdf[1:length(prot1),colnames(newdf) != "Sequence"]
for(i in 1:length(prot1)){
## grep for total intensity () includes non unique peps
protdf[i,1:input$chans] <- apply(newdf[grep(prot1[i],newdf$Accession),1:input$chans],2,sum,na.rm = TRUE)
protdf$Kd[i] <- sum(newdf$Kd[grep(prot1[i],newdf$Accession)],na.rm = TRUE)
protdf$Accession[i] <- prot1[i]
## use == to get unique peptides per protein per repeat
# protdf$uniquePeps[i] <- length(unique(newdf$Sequence[newdf$Accession == prot1[i]]))
protdf$uniquePeps[i] <- length(unique(unique(newdf$Sequence[newdf$Accession == prot1[i]])))
}
protdf$uniquePeps[grep(";",protdf$Accession)] <- 0
fc1 <- protdf[,1] / protdf[,2:input$chans]
Kd <- protdf$Kd / protdf[,1]
fcprotdf <- data.frame(log2(fc1),
Accession = protdf$Accession,uniquePepr1 = protdf$uniquePeps,
uniquePepr2 =protdf$uniquePeps, Kd = Kd)
fcprotdf<- fcprotdf[!is.na(rowSums(fcprotdf[1:(input$chans - 1 )])),]
fcprotdf
}else{
prot1 <- unique(newdf$Accession)
protdf<- newdf[1:length(prot1),colnames(newdf) != "Sequence"]
for(i in 1:length(prot1)){
## grep for total intensity () includes non unique peps
protdf[i,1:input$chans] <- apply(newdf[grep(prot1[i],newdf$Accession),1:input$chans],2,sum,na.rm = TRUE)
protdf$Accession[i] <- prot1[i]
## use == to get unique peptides per protein per repeat
# protdf$uniquePeps[i] <- length(unique(newdf$Sequence[newdf$Accession == prot1[i]]))
protdf$uniquePeps[i] <- length(unique(unique(newdf$Sequence[newdf$Accession == prot1[i]])))
}
protdf$uniquePeps[grep(";",protdf$Accession)] <- 0
fc1 <- protdf[,1] / protdf[,2:input$chans]
fcprotdf <- data.frame(log2(fc1),
Accession = protdf$Accession,uniquePepr1 = protdf$uniquePeps,
uniquePepr2 =protdf$uniquePeps)
fcprotdf<- fcprotdf[!is.na(rowSums(fcprotdf[1:(input$chans - 1 )])),]
fcprotdf
}
}else{
prot1 <- unique(newdf$Accession)
protdf<- newdf[1:length(prot1),colnames(newdf) != "Sequence"]
for(i in 1:length(prot1)){
## grep for total intensity () includes non unique peps
protdf[i,1:input$chans] <- apply(newdf[grep(prot1[i],newdf$Accession),1:input$chans],2,sum,na.rm = TRUE)
protdf$Accession[i] <- prot1[i]
## use == to get unique peptides per protein per repeat
# protdf$uniquePeps[i] <- length(unique(newdf$Sequence[newdf$Accession == prot1[i]]))
protdf$uniquePeps[i] <- length(unique(c(unique(newdf$Sequence[newdf$Accession == prot1[i]]),unique(newdf2$Sequence[newdf2$Accession == prot1[i]]))))
}
protdf$uniquePeps[grep(";",protdf$Accession)] <- 0
prot2 <- unique(newdf2$Accession)
### second data frame
protdf2<- newdf2[1:length(prot2),colnames(newdf2) != "Sequence"]
for(i in 1:length(prot2)){
## grep for total intensity () includes non unique peps
protdf2[i,1:input$chans] <- apply(newdf2[grep(prot2[i],newdf2$Accession),1:input$chans],2,median,na.rm = TRUE)
protdf2$Accession[i] <- prot2[i]
## use == to get unique peptides per protein per repeat
protdf2$uniquePeps[i] <- length(unique(newdf2$Sequence[newdf2$Accession == prot2[i]]))
}
protdf2$uniquePeps[grep(";",protdf2$Accession)] <- 0
com.prot <- intersect(protdf$Accession,protdf2$Accession)
fc1 <- protdf[,1] / protdf[,2:input$chans]
fc2 <- protdf2[,1] / protdf2[,2:input$chans]
fcprotdf <- data.frame(log2(fc1[match(com.prot,protdf$Accession),]),
log2(fc2[match(com.prot,protdf2$Accession),]),
Accession = com.prot,uniquePepr1 = protdf$uniquePeps[match(com.prot,protdf$Accession)],
uniquePepr2 =protdf2$uniquePeps[match(com.prot,protdf2$Accession)])
fcprotdf<- fcprotdf[!is.na(rowSums(fcprotdf[1:(input$reps*input$chans -2 )])),]
fcprotdf
}
}else{
totpepdf <- NULL
totpepdf2 <- NULL
for (z in 1:length(common.proteins)){
temp <- newdf[newdf$Accession == common.proteins[z],]
temp2 <- newdf2[newdf2$Accession == common.proteins[z],]
# first step: check if all peptides are unique ...
if(all.equal(grep(";",temp$Accession),integer(0)) == TRUE){
uniPeptides1 <- length(unique(temp$Sequence))
} else {
uniPeptides1 <- length(unique(temp$Sequence[-grep(";",temp$Accession)]))
}
if(all.equal(grep(";",temp2$Accession),integer(0)) == TRUE){
uniPeptides2 <- length(unique(temp2$Sequence))
}else{
uniPeptides2 <- length(unique(temp2[-grep(";",temp2$Accession)]))
}
## add unique peptide column
temp$uniquePeps <- uniPeptides1
temp2$uniquePeps <- uniPeptides2
tempPep <- intersect(unique(temp$Sequence),unique(temp2$Sequence))
if(all.equal(tempPep, character(0)) == TRUE){
next
}
for(i in 1:length(tempPep)){
if(sum(temp$Sequence == tempPep[i]) != sum(temp2$Sequence == tempPep[i])){
dr <- peptide.match(temp[temp$Sequence == tempPep[i],],temp2[temp2$Sequence == tempPep[i],],input$chans)
dr1 <- dr$dr1
dr2 <- dr$dr2
} else {
dr1 <- temp[temp$Sequence == tempPep[i],]
dr2 <- temp2[temp2$Sequence == tempPep[i],]
}
tempoindex <- rep(FALSE,nrow(dr1))
for(j in 1:nrow(dr1)){
percor <- cor.test(log2(as.numeric(dr1[j,1:input$chans])),log2(as.numeric(dr2[j,1:input$chans])))
tempoindex[j] <- percor$estimate < input$pearsvar
}
dr1[tempoindex,1:input$chans] <- NA
dr2[tempoindex,1:input$chans] <- NA
tempReplace <- dr1
tempReplace2 <- dr2
temp <- temp[temp$Sequence != tempPep[i],]
temp <- rbind(temp,tempReplace)
temp2 <- temp2[temp2$Sequence != tempPep[i],]
temp2 <- rbind(temp2,tempReplace2)
}
temp<- temp[match(tempPep,temp$Sequence),]
temp2<- temp2[match(tempPep,temp2$Sequence),]
# newdf <- newdf[newdf$Accession != common.proteins[z],]
# newdf<- rbind(newdf,temp)
totpepdf <- rbind(totpepdf,temp)
# newdf2 <- newdf2[newdf2$Accession != common.proteins[z],]
# newdf2<- rbind(newdf2,temp2)
totpepdf2 <- rbind(totpepdf2,temp2)
}
totpepdf<- totpepdf[!is.na(rowSums(totpepdf[,1:input$chans])),]
totpepdf2<- totpepdf2[!is.na(rowSums(totpepdf2[,1:input$chans])),]
totpepdf<- totpepdf[totpepdf$addedVals == 0, ]
totpepdf<- totpepdf[totpepdf$addedVals == 0, ]
totpepdf$uniquePeps[grep(';',totpepdf$Accession)] <- 0
### take sums
pepframe<- data.frame(totpepdf[1:length(common.proteins),1:input$chans],totpepdf2[1:length(common.proteins),1:input$chans],
Accession = totpepdf$Accession[1:length(common.proteins)], uniquePeps = totpepdf$uniquePeps[1:length(common.proteins)])
pepsum1 <- pepsum2 <- totpepdf[1:length(common.proteins),]
pepsum1 <- pepsum1[,-match(c("Sequence","addedVals", "Quality","outliers"),colnames(pepsum1))]
pepsum2 <- pepsum2[,-match(c("Sequence","addedVals", "Quality","outliers"),colnames(pepsum2))]
pepsum1$pepNum <- pepsum1$pepNum <- rep(0,length(common.proteins))
colnames(pepsum2)[1:input$chans]<- channelnames[(input$chans+1):(input$chans*input$reps)]
for(i in 1:length(common.proteins)){
pepsum1[i,1:input$chans] <- colSums(totpepdf[grep(common.proteins[i],totpepdf$Accession),1:input$chans])
pepsum2[i,1:input$chans] <- colSums(totpepdf2[grep(common.proteins[i],totpepdf2$Accession),1:input$chans])
pepsum1$pepNum[i] <- nrow(totpepdf[grep(common.proteins[i],totpepdf$Accession),1:input$chans])
pepsum2$pepNum[i] <- nrow(totpepdf2[grep(common.proteins[i],totpepdf2$Accession),1:input$chans])
pepsum1$Accession[i]<- pepsum2$Accession[i] <- common.proteins[i]
pepsum1$uniquePeps[i]<- totpepdf$uniquePeps[as.logical(match(totpepdf$Accession,common.proteins[i],nomatch = FALSE))][1]
# pepframe[i, 1:input$chans] <- apply( totpepdf[totpepdf$Accession == common.proteins[i], 1:input$chans],2, sum)
# pepframe[i, (input$chans+1):(input$chans*input$reps)] <- apply( totpepdf2[totpepdf2$Accession == common.proteins[i], 1:input$chans],2, sum)
#
# pepframe$Accession <- common.proteins[i]
# pepframe$uniquePeps <- totpepdf$uniquePeps[totpepdf$Accession == common.proteins[i]][1]
}
indexpepsum <- ((rowSums(pepsum1[1:input$chans]) != 0) + ((rowSums(pepsum2[1:input$chans])) != 0)) == 2
pepsum1<- pepsum1[indexpepsum, ]
pepsum2<- pepsum2[indexpepsum, ]
# indpepsum2 <- pepsum1$pepNum > 1 | pepsum2$pepNum > 1
# pepsum1 <- pepsum1[indpepsum2,]
# pepsum2 <- pepsum1[indpepsum2,]
fc1 <- pepsum1[,1] / pepsum1[,2:input$chans]
fc2 <- pepsum2[,1] / pepsum2[,2:input$chans]
fcprotdf <- data.frame(log2(fc1),log2(fc2),pepsum1$Accession,uniquePepr1 = pepsum1$uniquePeps,
uniquePepr2 = pepsum2$uniquePeps,num1 = pepsum1$pepNum, num2 = pepsum2$pepNum )
fcprotdf
}
fcprotdf
}else{
return(NULL)
}
})
######################################################### isolate removed peptides
pepdwn <- reactive({
if(input$intcalc == 0){
return(NULL)
}else{
tempdat <- data()
# make matrix of descriptions and accessions to filter by common proteins
accDesMat<- as.character(tempdat[as.character(tempdat[,input$accession]) == "",c(input$accession)])
data.merged <- tempdat[,c(input$view_vars, input$accession, input$sequence,input$quality)]
channelnames <- standardNames()
repindex <- rep(1:input$reps,each = input$chans)
totfal <- rep(FALSE , (input$chans + 3 ))
newdf <- cbind(data.merged[,1:input$chans], data.merged[,c(input$accession, input$sequence,input$quality)])
colnames(newdf) <- c(channelnames[repindex == 1],"Accession","Sequence", "Quality")
newdf <- newdf[!is.na(rowSums(newdf[,1:input$chans])),]
newdf <- newdf[newdf$Quality <= 0.05, ]
newdf2 <- cbind(data.merged[,(input$chans+1):(2*input$chans) ],data.merged[,c(input$accession, input$sequence,input$quality)])
colnames(newdf2) <- c(channelnames[repindex == 2],"Accession","Sequence","Quality")
newdf2 <- newdf2[!is.na(rowSums(newdf2[,1:input$chans])),]
newdf2 <- newdf2[newdf2$Quality <= 0.05, ]
newdf <- data.frame(newdf, outliers = rep(0,length(newdf[,1])), uniquePeps = rep(0,length(newdf[,1])), addedVals = rep(0,length(newdf[,1])))
newdf2 <- data.frame(newdf2, outliers = rep(0,length(newdf2[,1])), uniquePeps = rep(0,length(newdf2[,1])), addedVals = rep(0,length(newdf2[,1])))
common.proteins <- intersect(unique(newdf$Accession),unique(newdf2$Accession))
newdf <- newdf[!is.na(match(newdf$Accession,common.proteins)),]
newdf2 <- newdf2[!is.na(match(newdf2$Accession,common.proteins)),]
totpepdf <- NULL
totpepdf2 <- NULL
for (z in 1:length(common.proteins)){
temp <- newdf[newdf$Accession == common.proteins[z],]
temp2 <- newdf2[newdf2$Accession == common.proteins[z],]
# first step: check if all peptides are unique ...
if(all.equal(grep(";",temp$Accession),integer(0)) == TRUE){
uniPeptides1 <- length(unique(temp$Sequence))
} else {
uniPeptides1 <- length(unique(temp$Sequence[-grep(";",temp$Accession)]))
}
if(all.equal(grep(";",temp2$Accession),integer(0)) == TRUE){
uniPeptides2 <- length(unique(temp2$Sequence))
}else{
uniPeptides2 <- length(unique(temp2[-grep(";",temp2$Accession)]))
}
## add unique peptide column
temp$uniquePeps <- uniPeptides1
temp2$uniquePeps <- uniPeptides2
tempPep <- intersect(unique(temp$Sequence),unique(temp2$Sequence))
if(all.equal(tempPep, character(0)) == TRUE){
next
}
for(i in 1:length(tempPep)){
if(sum(temp$Sequence == tempPep[i]) != sum(temp2$Sequence == tempPep[i])){
dr <- peptide.match(temp[temp$Sequence == tempPep[i],],temp2[temp2$Sequence == tempPep[i],],input$chans)
dr1 <- dr$dr1
dr2 <- dr$dr2
} else {
dr1 <- temp[temp$Sequence == tempPep[i],]
dr2 <- temp2[temp2$Sequence == tempPep[i],]
}
tempoindex <- rep(FALSE,nrow(dr1))
for(j in 1:nrow(dr1)){
percor <- cor.test(log2(as.numeric(dr1[j,1:input$chans])),log2(as.numeric(dr2[j,1:input$chans])))
tempoindex[j] <- percor$estimate < input$pearsvar
}
dr1[tempoindex,1:input$chans] <- NA
dr2[tempoindex,1:input$chans] <- NA
tempReplace <- dr1
tempReplace2 <- dr2
temp <- temp[temp$Sequence != tempPep[i],]
temp <- rbind(temp,tempReplace)
temp2 <- temp2[temp2$Sequence != tempPep[i],]
temp2 <- rbind(temp2,tempReplace2)
}
temp<- temp[match(tempPep,temp$Sequence),]
temp2<- temp2[match(tempPep,temp2$Sequence),]
# newdf <- newdf[newdf$Accession != common.proteins[z],]
# newdf<- rbind(newdf,temp)
totpepdf <- rbind(totpepdf,temp)
# newdf2 <- newdf2[newdf2$Accession != common.proteins[z],]
# newdf2<- rbind(newdf2,temp2)
totpepdf2 <- rbind(totpepdf2,temp2)
}
totpepdf<- totpepdf[!is.na(rowSums(totpepdf[,1:input$chans])),]
totpepdf2<- totpepdf2[!is.na(rowSums(totpepdf2[,1:input$chans])),]
totpepdf<- totpepdf[totpepdf$addedVals == 0, ]
totpepdf<- totpepdf[totpepdf$addedVals == 0, ]
totpepdf$uniquePeps[grep(';',totpepdf$Accession)] <- 0
### take sums
pepframe<- data.frame(totpepdf[1:length(common.proteins),1:input$chans],totpepdf2[1:length(common.proteins),1:input$chans],
Accession = totpepdf$Accession[1:length(common.proteins)], uniquePeps = totpepdf$uniquePeps[1:length(common.proteins)])
pepsum1 <- pepsum2 <- totpepdf[1:length(common.proteins),]
pepsum1 <- pepsum1[,-match(c("Sequence","addedVals", "Quality","outliers"),colnames(pepsum1))]
pepsum2 <- pepsum2[,-match(c("Sequence","addedVals", "Quality","outliers"),colnames(pepsum2))]
pepsum1$pepNum <- pepsum1$pepNum <- rep(0,length(common.proteins))
colnames(pepsum2)[1:input$chans]<- channelnames[(input$chans+1):(input$chans*input$reps)]
for(i in 1:length(common.proteins)){
pepsum1[i,1:input$chans] <- colSums(totpepdf[grep(common.proteins[i],totpepdf$Accession),1:input$chans])
pepsum2[i,1:input$chans] <- colSums(totpepdf2[grep(common.proteins[i],totpepdf2$Accession),1:input$chans])
pepsum1$pepNum[i] <- nrow(totpepdf[grep(common.proteins[i],totpepdf$Accession),1:input$chans])
pepsum2$pepNum[i] <- nrow(totpepdf2[grep(common.proteins[i],totpepdf2$Accession),1:input$chans])
pepsum1$Accession[i]<- pepsum2$Accession[i] <- common.proteins[i]
pepsum1$uniquePeps[i]<- totpepdf$uniquePeps[as.logical(match(totpepdf$Accession,common.proteins[i],nomatch = FALSE))][1]
}
indexpepsum <- ((rowSums(pepsum1[1:input$chans]) != 0) + ((rowSums(pepsum2[1:input$chans])) != 0)) == 2
pepsum1<- pepsum1[indexpepsum, ]
pepsum2<- pepsum2[indexpepsum, ]
end <- -row.match(newdf[,1:(input$chans+2)],totpepdf[,1:(input$chans+2)])
end2 <- -row.match(newdf2[,1:(input$chans+2)],totpepdf2[,1:(input$chans+2)])
rempep <- newdf[end,]
rempep2 <- newdf2[end2,]
colnames(rempep)<- paste("r1_",colnames(rempep),sep = '')
colnames(rempep2)<- paste("r2_",colnames(rempep2),sep = '')
if(nrow(rempep) > nrow(rempep2)){
finalrempep <- rempep
finalrempep[] <- NA
finalrempep[1:nrow(rempep2),]<- rempep2
finalrempep<- cbind(rempep,finalrempep)
}else{
finalrempep <- rempep2
finalrempep[] <- NA
finalrempep[1:nrow(rempep),] <- rempep
finalrempep <- cbind(finalrempep,rempep2)
}
colnames(finalrempep)<- c(paste("r1_",colnames(rempep),sep = ''),paste("r2_",colnames(rempep2),sep = ''))
finalrempep
}
})
## log fold changes
dataMerge <- reactive({
# testingkd <- rKd()
# print(head(testingkd))
inten <- intData()
if(input$datype != "intensity"){
if(input$modtyp == "sigmoid"){
data_orig2 <- data()
## if user has specified accession & Description
if(input$toacc == FALSE){
pattern<-"GN=(\\S+)"
g_fromD1<-str_extract(data_orig2$Description,pattern)
gID_D1a<-str_split_fixed(g_fromD1,"GN=",n=2)
gID_D1a<-as.vector(gID_D1a[,2])
gID_D1<-as.matrix(replace(gID_D1a,gID_D1a=="","NA"))
#Addition of the gene ID column
data_orig2["geneID"]<- (gID_D1)
}else{
if(input$genefile == FALSE){
tempacc <- data_orig2[,input$accession]
data_orig2 <- data_orig2[,(-input$accession)]
data_orig2$Accession <- tempacc
uniGene <- uniprotGene()
#uniGene$Gene.names <- gsub(' .*','',uniGene$Gene.names)
uniGene$Gene.names[uniGene$Gene.names == '']<- NA
GeneID <- uniGene$Gene.names[match(data_orig2$Accession,uniGene$Entry)]
GeneID <- make.names(GeneID,unique = TRUE)
data_orig2$geneID <- GeneID
}else{
tempacc <- data_orig2[,input$accession]
data_orig2 <- data_orig2[,(-input$accession)]
data_orig2$Accession <- tempacc
uniGene <- uploadGene()
GeneID <- uniGene$Gene.names[match(data_orig2$Accession,uniGene$Entry)]
GeneID <- make.names(GeneID,unique = TRUE)
data_orig2$geneID <- GeneID
data_orig2<-na.omit(data_orig2)
}
}
if(input$incpd == TRUE){
if(input$toacc == FALSE){
data.merged<-data.frame(data_orig2[,input$view_vars],
data_orig2$Accession, data_orig2$geneID,
data_orig2$X..Unique.Peptides,data_orig2[,input$pdofpd])
}else{
data.merged<-data.frame(data_orig2[,input$view_vars],
data_orig2$Accession, data_orig2$geneID,
data_orig2[,input$unipeps],data_orig2[,input$pdofpd])
}
final.Names <- finalNames()
colnames(data.merged)<- c(final.Names,
"Accession", "GeneID","UniquePeps",'Kd')
tmp<-data.merged[,1:input$chans]
tf <- as.data.frame(lapply(tmp, function(x) (is.na(x))))
countsNAs<-as.data.frame(apply(tf,1,function(x)table(x)["TRUE"]))
n_of_miss<-as.data.frame(as.numeric(str_replace_all(as.list(countsNAs[,1]),"NA",'0')))
data.merged <- data.frame(data.merged,n_of_miss)
colnames(data.merged)<-c( final.Names,
"Accession", "GeneID","UniquePeps",'Kd', "MissingVal")
#
missing_val <- 0
#
data.merged<- as.data.frame(data.merged[data.merged$MissingVal <= missing_val, ])
data.merged<-na.omit(data.merged)
#
# #Specify the number of missing points.For zero missing point is ==0
#
# #filiter for 2 unique peptides
data.merged <- data.merged[data.merged$UniquePeps > 1, ]
data.merged<-na.omit(data.merged)
#
#
if(input$normalize == 'loess' ){
data.merged <- data.frame(log2(normalize.loess(2^(data.merged[,channels()]))),
Accession=data.merged$Accession,
GeneID=data.merged$GeneID,
UniquePeps=data.merged$UniquePeps,
Kd = 1 / data.merged$Kd,
MissingVal=data.merged$MissingVal)
}else if(input$normalize == 'median'){
data.merged <- data.frame(log2( sweep( (2^(data.merged[,channels()]) ) ,
MARGIN = 2,
as.numeric(apply((2^(data.merged[,channels()])),2,median)),
FUN = "/")
),
Accession=data.merged$Accession,
GeneID=data.merged$GeneID,
UniquePeps=data.merged$UniquePeps,
Kd = 1 / data.merged$Kd,
MissingVal=data.merged$MissingVal)
}else{
data.merged <- data.frame(((2^(data.merged[,channels()]))),
Accession=data.merged$Accession,
GeneID=data.merged$GeneID,
UniquePeps=data.merged$UniquePeps,
Kd = 1 / data.merged$Kd,
MissingVal=data.merged$MissingVal)
}
data.merged<-na.omit(data.merged)
data.merged
} else {
if(input$toacc == FALSE){
data.merged<-data.frame(data_orig2[,input$view_vars],
data_orig2$Accession, data_orig2$geneID,
data_orig2$X..Unique.Peptides)
}else{
data.merged<-data.frame(data_orig2[,input$view_vars],
data_orig2$Accession, data_orig2$geneID,
data_orig2[,input$unipeps])
}
final.Names <- finalNames()
colnames(data.merged)<- c(final.Names,
"Accession", "GeneID","UniquePeps")
tmp<-data.merged[,1:input$chans]
tf <- as.data.frame(lapply(tmp, function(x) (is.na(x))))
countsNAs<-as.data.frame(apply(tf,1,function(x)table(x)["TRUE"]))
n_of_miss<-as.data.frame(as.numeric(str_replace_all(as.list(countsNAs[,1]),"NA",'0')))
data.merged <- data.frame(data.merged,n_of_miss)
colnames(data.merged)<-c( final.Names,
"Accession", "GeneID","UniquePeps","MissingVal")
#
missing_val <- 0
#
data.merged<- as.data.frame(data.merged[data.merged$MissingVal <= missing_val, ])
#
# #Specify the number of missing points.For zero missing point is ==0
#
# #filiter for 2 unique peptides
data.merged <- data.merged[data.merged$UniquePeps > 1, ]
#
#
if(input$normalize == 'loess'){
data.merged <- data.frame(log2(normalize.loess(2^(data.merged[,channels()]))),
Accession=data.merged$Accession,
GeneID=data.merged$GeneID,
UniquePeps=data.merged$UniquePeps,
MissingVal=data.merged$MissingVal)
}else if (input$normalize == 'median'){
data.merged <- data.frame(log2( sweep( (2^(data.merged[,channels()]) ) ,
MARGIN = 2,
as.numeric(apply((2^(data.merged[,channels()])),2,median)),
FUN = "/")
),
Accession=data.merged$Accession,
GeneID=data.merged$GeneID,
UniquePeps=data.merged$UniquePeps,
MissingVal=data.merged$MissingVal)
}else{
data.merged <- data.frame(log2(2^(data.merged[,channels()])),
Accession=data.merged$Accession,
GeneID=data.merged$GeneID,
UniquePeps=data.merged$UniquePeps,
MissingVal=data.merged$MissingVal)
}
data.merged<-na.omit(data.merged)
data.merged
}
} else {
tempdat <- data()
temp<- channels()
nvec <- length(temp)
data.merged <- tempdat[,input$view_vars]
colnames(data.merged) <- finalNames()
data.names<- c(input$view_vars,"Accession", "GeneID","UniquePeps","MissingVal")
if(input$datype == "FC"){
data.merged[,temp] <- log2(data.merged[,temp])
}
#tidy below !!
if(input$toacc == FALSE){
pattern<-"GN=(\\S+)"
g_fromD1<-str_extract(tempdat$Description,pattern)
gID_D1a<-str_split_fixed(g_fromD1,"GN=",n=2)
gID_D1a<-as.vector(gID_D1a[,2])
gID_D1<-as.matrix(replace(gID_D1a,gID_D1a=="","NA"))
Accession <- tempdat$Accession
UniquePeps <- MissingVal<- tempdat[,grep("Unique",colnames(tempdat))]
data.merged <- cbind(data.merged,Accession, GeneID = gID_D1,UniquePeps,MissingVal)
data.merged<-na.omit(data.merged)
} else {
tempdat$Accession <- tempdat[,input$accession]
if(input$genefile == FALSE){
uniGene <- uniprotGene()
# uniGene<- as.data.frame(uniGene,stringsAsFactors = FALSE)
#uniGene$Gene.names <- gsub(' .*','',uniGene$Gene.names)
print(head(uniGene))
} else{
uniGene <- uploadGene()
colnames(uniGene)[1:2] <- c('Entry','Gene.names')
}
uniGene$Gene.names[uniGene$Gene.names == '']<- NA
GeneID <- uniGene$Gene.names[match(tempdat$Accession,uniGene$Entry)]
GeneID <- make.names(GeneID,unique = TRUE)
print(GeneID)
Accession <- tempdat$Accession
UniquePeps <- MissingVal<- tempdat[,input$unipeps]
# data_orig2$geneID <- GeneID
data.merged <- cbind(data.merged,Accession, GeneID = GeneID,UniquePeps,MissingVal)
data.merged<-na.omit(data.merged)
print(head(data.merged))
}
missing<- rowSums(is.na(data.merged[,channels()]))
missing_val <- 0
data.merged$MissingVal <- missing
## subset by missing
data.merged <- data.merged[data.merged$MissingVal <= missing_val, ]
data.merged<- as.data.frame(data.merged[data.merged$MissingVal <= missing_val, ])
data.merged <- data.merged[data.merged$UniquePeps > 1, ]
data.merged<-na.omit(data.merged)
#
#
if(input$normalize == 'loess'){
data.merged <- data.frame(log2(normalize.loess(2^(data.merged[,channels()]))),
Accession=data.merged$Accession,
GeneID=data.merged$GeneID,
UniquePeps=data.merged$UniquePeps,
MissingVal=data.merged$MissingVal)
}else if(input$normalize == 'median'){
data.merged <- data.frame(log2( sweep( (2^(data.merged[,channels()]) ) ,
MARGIN = 2,
as.numeric(apply((2^(data.merged[,channels()])),2,median)),
FUN = "/")
),
Accession=data.merged$Accession,
GeneID=data.merged$GeneID,
UniquePeps=data.merged$UniquePeps,
MissingVal=data.merged$MissingVal)
}else{
data.merged <- data.frame(log2((2^(data.merged[,channels()]))),
Accession=data.merged$Accession,
GeneID=data.merged$GeneID,
UniquePeps=data.merged$UniquePeps,
MissingVal=data.merged$MissingVal)
}
data.merged<-na.omit(data.merged)
data.merged
## filter for 2 unique peptide
}
} else {
### intensities to protein done.. here no description so we need toi use accession and intermine
tempdat <- inten
if(input$genefile == FALSE){
uniGene <- uniprotGene()
#uniGene$Gene.names <- gsub(' .*','',uniGene$Gene.names)
}else{
uniGene <- uploadGene()
colnames(uniGene) <- c('Entry','Gene.names')
}
if(input$dorem =='yes'){
Accession <- tempdat$pepsum1.Accession
}else{
Accession <- tempdat$Accession
}
uniGene$Gene.names[uniGene$Gene.names == '']<- NA
GeneID <- uniGene$Gene.names[match(Accession,uniGene$Entry)]
GeneID <- make.names(GeneID,unique = TRUE)
tempdat$GeneID <- GeneID
UniquePeps <- tempdat$uniquePepr1
if(input$reps == 1){
data.merged <- tempdat
final.Names <- paste0('rep1_C',0:(input$chans - 2))
if(input$incpd == TRUE){
data.merged <- data.frame(data.merged[,1:(input$chans -1 )], Accession = data.merged$Accession,
GeneID = data.merged$GeneID, UniquePeps = data.merged$uniquePepr1, Kd = data.merged$Kd)
colnames(data.merged)<- c(final.Names,
"Accession", "GeneID","UniquePeps", 'Kd')
tmp<-data.merged[,1:(input$chans -1 )]
tf <- as.data.frame(lapply(tmp, function(x) (is.na(x))))
countsNAs<-as.data.frame(apply(tf,1,function(x)table(x)["TRUE"]))
n_of_miss<-as.data.frame(as.numeric(str_replace_all(as.list(countsNAs[,1]),"NA",'0')))
data.merged <- data.frame(data.merged,n_of_miss)
colnames(data.merged)<-c( final.Names,
"Accession", "GeneID","UniquePeps",'Kd',"MissingVal")
#
missing_val <- 0
#
data.merged<- as.data.frame(data.merged[data.merged$MissingVal <= missing_val, ])
#
# #Specify the number of missing points.For zero missing point is ==0
#
# #filiter for 2 unique peptides
data.merged <- data.merged[data.merged$UniquePeps > 1, ]
#
#
if(input$normalize == 'loess'){
data.merged <- data.frame(log2(normalize.loess(2^(data.merged[,1:(input$chans -1)]))),
Accession=data.merged$Accession,
GeneID=data.merged$GeneID,
UniquePeps=data.merged$UniquePeps,
Kd = data.merged$Kd
)
}else if(input$normalize == 'median'){
data.merged <- data.frame(log2( sweep( (2^(data.merged[,1:(input$chans -1)]) ) ,
MARGIN = 2,
as.numeric(apply((2^(data.merged[,1:(input$chans -1)])),2,median)),
FUN = "/")
),
Accession=data.merged$Accession,
GeneID=data.merged$GeneID,
UniquePeps=data.merged$UniquePeps,
Kd = data.merged$Kd
)
}else{
data.merged <- data.frame(log2(2^(data.merged[,1:(input$chans -1)])),
Accession=data.merged$Accession,
GeneID=data.merged$GeneID,
UniquePeps=data.merged$UniquePeps,
Kd = data.merged$Kd
)
}
data.merged<-na.omit(data.merged)
data.merged
} else {
data.merged <- data.frame(data.merged[,1:(input$chans -1 )], Accession = data.merged$Accession,
GeneID = data.merged$GeneID, UniquePeps = data.merged$uniquePepr1)
colnames(data.merged)<- c(final.Names,
"Accession", "GeneID","UniquePeps")
tmp<-data.merged[,1:(input$chans -1 )]
tf <- as.data.frame(lapply(tmp, function(x) (is.na(x))))
countsNAs<-as.data.frame(apply(tf,1,function(x)table(x)["TRUE"]))
n_of_miss<-as.data.frame(as.numeric(str_replace_all(as.list(countsNAs[,1]),"NA",'0')))
data.merged <- data.frame(data.merged,n_of_miss)
colnames(data.merged)<-c( final.Names,
"Accession", "GeneID","UniquePeps","MissingVal")
#
missing_val <- 0
#
data.merged<- as.data.frame(data.merged[data.merged$MissingVal <= missing_val, ])
#
# #Specify the number of missing points.For zero missing point is ==0
#
# #filiter for 2 unique peptides
data.merged <- data.merged[data.merged$UniquePeps > 1, ]
#
#
if(input$normalize == 'loess'){
data.merged <- data.frame(log2(normalize.loess(2^(data.merged[,1:(input$chans -1)]))),
Accession=data.merged$Accession,
GeneID=data.merged$GeneID,
UniquePeps=data.merged$UniquePeps)
}else if(input$normalize == 'median'){
data.merged <- data.frame(log2( sweep( (2^(data.merged[,1:(input$chans -1)]) ) ,
MARGIN = 2,
as.numeric(apply((2^(data.merged[,1:(input$chans -1)])),2,median)),
FUN = "/")
),
Accession=data.merged$Accession,
GeneID=data.merged$GeneID,
UniquePeps=data.merged$UniquePeps)
}else{
data.merged <- data.frame(log2(((2^(data.merged[,1:(input$chans -1)])))),
Accession=data.merged$Accession,
GeneID=data.merged$GeneID,
UniquePeps=data.merged$UniquePeps)
}
data.merged<-na.omit(data.merged)
data.merged
}
} else{
data.merged <- tempdat[,1:(input$chans*input$reps - 2)]
data.merged <- tempdat[,1:(input$chans*input$reps - 2)]
if( input$dorem == 'no'){
Accession <- tempdat$Accession
MissingVal <- UniquePeps
data.merged <- cbind(data.merged,Accession, GeneID = GeneID,UniquePeps,MissingVal)
data.merged <- data.merged[!is.na(rowSums(data.merged[,1:(input$chans*input$reps -2)])),]
#PR add the na.omit
data.merged <- na.omit(data.merged[data.merged$UniquePeps > 1, ])
if(input$normalize == 'loess'){
data.merged <- data.frame((log2(normalize.loess(2^(data.merged[,1:(input$chans*input$reps - 2)])))),
Accession=data.merged$Accession,
GeneID=data.merged$GeneID,
UniquePeps=data.merged$UniquePeps)
}else if(input$normalize == 'median'){
data.merged <- data.frame(log2( sweep( (2^(data.merged[,1:(input$chans*input$reps - 2)]) ) ,
MARGIN = 2,
as.numeric(apply((2^(data.merged[,1:(input$chans*input$reps - 2)])),2,median)),
FUN = "/")
),
Accession=data.merged$Accession,
GeneID=data.merged$GeneID,
UniquePeps=data.merged$UniquePeps)
}else{
data.merged <- data.frame((log2((2^(data.merged[,1:(input$chans*input$reps - 2)])))),
Accession=data.merged$Accession,
GeneID=data.merged$GeneID,
UniquePeps=data.merged$UniquePeps)
}
data.merged <- data.merged[!is.na(rowSums(data.merged[,1:(input$chans*input$reps -2)])),]
data.merged<-na.omit(data.merged)
data.merged
}else{
Accession <- tempdat$pepsum1.Accession
data.merged <- cbind(data.merged,Accession, GeneID = GeneID,UniquePeps, num1 = tempdat$num1, num2 = tempdat$num2)
data.merged <- data.merged[!is.na(rowSums(data.merged[,1:(input$chans*input$reps -2)])),]
#PR add the na.omit
data.merged <- na.omit(data.merged[data.merged$UniquePeps > 1, ])
if(input$normalize == 'loess'){
data.merged <- data.frame((log2(normalize.loess(2^(data.merged[,1:(input$chans*input$reps - 2)])))),
Accession=data.merged$Accession,
GeneID=data.merged$GeneID,
UniquePeps=data.merged$UniquePeps, num1 = data.merged$num1, num2 = data.merged$num2)
}else if(input$normalize == 'median'){
data.merged <- data.frame(log2( sweep( (2^(data.merged[,1:(input$chans*input$reps - 2)]) ) ,
MARGIN = 2,
as.numeric(apply((2^(data.merged[,1:(input$chans*input$reps - 2)])),2,median)),
FUN = "/")
),
Accession=data.merged$Accession,
GeneID=data.merged$GeneID,
UniquePeps=data.merged$UniquePeps, num1 = data.merged$num1, num2 = data.merged$num2)
}else{
data.merged <- data.frame((log2((2^(data.merged[,1:(input$chans*input$reps - 2)])))),
Accession=data.merged$Accession,
GeneID=data.merged$GeneID,
UniquePeps=data.merged$UniquePeps, num1 = data.merged$num1, num2 = data.merged$num2)
}
data.merged <- data.merged[data.merged$num1 > 1 | data.merged$num2 > 1 , ]
data.merged <- data.merged[!is.na(rowSums(data.merged[,1:(input$chans*input$reps -2)])),]
data.merged<-na.omit(data.merged)
data.merged
}
}
}
data.merged<-na.omit(data.merged)
data.merged
})
sigFinalNames <- reactive({
paste0("C_",1:input$chans)
})
sigPredNames <- reactive({
paste0("predX",1:input$chans)
})
dataMerge2 <- reactive({
nvec <- channels()
nvec <- length(nvec)
data.merged <- dataMerge()
if(input$modtyp == "sigmoid"){
if(input$datype == 'intensity'){
conc <- sigConc()
if(input$incpd == TRUE){
final.Names <- paste0('rep1_C',0:(input$chans - 2 ))
pred.names <- paste0('predX',1:(input$chans -1))
colnames(data.merged[,1:(input$chans -1)]) <- final.Names
data_merged_positives<- data.merged
data.merged<-na.omit(data.merged[data.merged[,1:input$chans] >= 1,])
data_merged_positives2<-( (1/data_merged_positives[,1:(input$chans -1 )]))*100
Reps_FC<-data.frame(data_merged_positives2 ,
Accession = data_merged_positives$Accession,GeneID = data_merged_positives$GeneID,
UniquePeps = data_merged_positives$UniquePeps, depletionConstant = data_merged_positives$Kd
)
ryegrass.m1<- vector(mode = "list",length = nrow(Reps_FC))
pvals<-list()
stderr<-list()
model_pred<-list()
coeff_predicted<-list()
for(i in 1:nrow(Reps_FC)){
#print(i)
#nrow(full_df_2)
#maxIt and relTol to be user defined
ryegrass.m1[[i]]<-try(drm(as.numeric(Reps_FC[i,1:(input$chans - 1 )]) ~ as.numeric(conc),
na.action = na.omit,
control = drmc(constr = FALSE, errorm = FALSE, noMessage = TRUE, maxIt = 1000, relTol = 1e-06),
fct = LL.4(fixed=c(NA, NA, NA, NA), #see note @top this file
names = c("Slope", "Lower Limit", "Upper Limit", "RB50"))),silent = TRUE)
}
failed_sigm=0
for(i in 1:length(ryegrass.m1)){
#print(i)
#checking_val if FALSE the model has failed to calculate the pval
checking_val<-try(is.numeric(coefficients(ryegrass.m1[[i]])[["Slope:(Intercept)"]]),silent = TRUE)
if(checking_val=="TRUE"){
#print(checking_val)
pvals[[i]]<-t(as.data.frame(summary(ryegrass.m1[[i]])$coefficients[13:16]))
colnames(pvals[[i]])<-c("SlopePval", "Lower_LimitPval", "Upper_LimitPval", "RB50Pval")
coeff_predicted[[i]]<-t(data.frame(coefficients(ryegrass.m1[[i]])))
colnames(coeff_predicted[[i]])<-c("SlopeCoef", "Lower_LimitCoef", "Upper_LimitCoef","RB50Coef")
stderr[[i]]<-t(as.data.frame(summary(ryegrass.m1[[i]])$coefficients[5:8]))
colnames(stderr[[i]])<-c("SlopeErr", "Lower_LimitErr", "Upper_LimitErr","RB50Err")
model_pred[[i]]<-predict(ryegrass.m1[[i]])
}else{
failed_sigm=failed_sigm+1
fit <- lm(as.numeric(Reps_FC[i,1:(input$chans -1)]) ~ poly(log10(conc),2 ))
#extract the pval
pval<-as.numeric(summary(fit)$coefficients[,4] )
pvals[[i]]<- t(as.data.frame(c(pval,"lm-fit:intercept.slope.quadratic") ))
colnames(pvals[[i]])<-c("SlopePval", "Lower_LimitPval", "Upper_LimitPval","RB50Pval")
stderr[[i]]<- data.frame(NA,NA,NA,NA)
colnames(stderr[[i]])<-c("SlopeErr", "Lower_LimitErr", "Upper_LimitErr","RB50Err")
coeff_predicted[[i]]<-data.frame(NA,NA,NA,NA)
colnames(coeff_predicted[[i]])<-c("SlopeCoef", "Lower_LimitCoef", "Upper_LimitCoef","RB50Coef")
model_pred[[i]]<- as.numeric(fitted(fit))
} #just adding NAs for the times the model failed
}
modelsReps<-data.frame(
do.call(rbind.data.frame,lapply(model_pred,function(x) as.numeric(x))),
Reps_FC$GeneID,
do.call(rbind.data.frame,lapply(pvals,function(x) x) ),
do.call(rbind.data.frame,lapply(coeff_predicted,function(x) x)) ,
do.call(rbind.data.frame,lapply(stderr,function(x) x) )
)
colnames(modelsReps)<-c(pred.names,"GeneID",
"SlopePval", "Lower_LimitPval","Upper_LimitPval", "RB50Pval",
"SlopeCoef", "Lower_LimitCoef","Upper_LimitCoef", "RB50Coef",
"SlopeErr", "Lower_LimitErr","Upper_LimitErr", "RB50Err"
)
data_merged_2 <-merge.data.frame(modelsReps,Reps_FC,by = 'GeneID')
data_merged_2<-data.frame(data_merged_2,"Top_minus_min"=data_merged_2$predX1-data_merged_2[,paste("predX",(input$chans-1),sep = "")])
crap <- crapome()
#
tempcrap <- crap$Gene
tempcrap<- crap$percentagePresent[match(data_merged_2$GeneID,crap$Gene)]
data_merged_2 <- data.frame(data_merged_2, CRAPomePercent = tempcrap)
proteome<-as.vector(toupper(data_merged_2$GeneID))
mykinases <- intersect(proteome,kinome)
if(!is.null(input$venninp)){
myvenninp <- uploadVenn()
uploadsInt <- intersect(proteome,myvenninp)
myvenvec <- match(proteome, uploadsInt, nomatch = NA)
## now combine with my kin vec
mykinvec <- match(proteome,mykinases, nomatch = NA)
mykinvec[!is.na(mykinvec) & !is.na(myvenvec)] <- 'KINASE + UPLOAD'
mykinvec[!is.na(mykinvec) & is.na(myvenvec)] <- 'KINASE'
mykinvec[is.na(mykinvec) & !is.na(myvenvec)] <- 'UPLOAD'
print(mykinvec)
} else {
mykinvec <- match(proteome,mykinases, nomatch = NA)
mykinvec[!is.na(mykinvec)]<- 'KINASE'
}
data_merged_2<- data.frame(data_merged_2, correctedRB50 = (data_merged_2$RB50Coef*data_merged_2$depletionConstant),Kinase = mykinvec)
data_merged_2
} else {
final.Names <- paste0('rep1_C',0:(input$chans - 2 ))
pred.names <- paste0('predX',1:(input$chans -1))
colnames(data.merged[,1:(input$chans -1)]) <- final.Names
data_merged_positives<- data.merged
# na.omit(data.merged[data.merged[,1:input$chans] >= 1,])
data_merged_positives2<-( (1/data_merged_positives[,1:(input$chans -1 )]))*100
Reps_FC<-data.frame(data_merged_positives2 ,
Accession = data_merged_positives$Accession,GeneID = data_merged_positives$GeneID,
UniquePeps = data_merged_positives$UniquePeps
)
ryegrass.m1<- vector(mode = "list",length = nrow(Reps_FC))
pvals<-list()
stderr<-list()
model_pred<-list()
coeff_predicted<-list()
for(i in 1:nrow(Reps_FC)){
#print(i)
#nrow(full_df_2)
#maxIt and relTol to be user defined
ryegrass.m1[[i]]<-try(drm(as.numeric(Reps_FC[i,1:(input$chans - 1 )]) ~ as.numeric(conc),
na.action = na.omit,
control = drmc(constr = FALSE, errorm = FALSE, noMessage = TRUE, maxIt = 1000, relTol = 1e-06),
fct = LL.4(fixed=c(NA, NA, NA, NA), #see note @top this file
names = c("Slope", "Lower Limit", "Upper Limit", "RB50"))),silent = TRUE)
}
failed_sigm=0
for(i in 1:length(ryegrass.m1)){
#print(i)
#checking_val if FALSE the model has failed to calculate the pval
checking_val<-try(is.numeric(coefficients(ryegrass.m1[[i]])[["Slope:(Intercept)"]]),silent = TRUE)
if(checking_val=="TRUE"){
#print(checking_val)
pvals[[i]]<-t(as.data.frame(summary(ryegrass.m1[[i]])$coefficients[13:16]))
colnames(pvals[[i]])<-c("SlopePval", "Lower_LimitPval", "Upper_LimitPval", "RB50Pval")
coeff_predicted[[i]]<-t(data.frame(coefficients(ryegrass.m1[[i]])))
colnames(coeff_predicted[[i]])<-c("SlopeCoef", "Lower_LimitCoef", "Upper_LimitCoef","RB50Coef")
stderr[[i]]<-t(as.data.frame(summary(ryegrass.m1[[i]])$coefficients[5:8]))
colnames(stderr[[i]])<-c("SlopeErr", "Lower_LimitErr", "Upper_LimitErr","RB50Err")
model_pred[[i]]<-predict(ryegrass.m1[[i]])
}else{
failed_sigm=failed_sigm+1
fit <- lm(as.numeric(Reps_FC[i,1:(input$chans -1)]) ~ poly(log10(conc),2 ))
#extract the pval
pval<-as.numeric(summary(fit)$coefficients[,4] )
pvals[[i]]<- t(as.data.frame(c(pval,"lm-fit:intercept.slope.quadratic") ))
colnames(pvals[[i]])<-c("SlopePval", "Lower_LimitPval", "Upper_LimitPval","RB50Pval")
stderr[[i]]<- data.frame(NA,NA,NA,NA)
colnames(stderr[[i]])<-c("SlopeErr", "Lower_LimitErr", "Upper_LimitErr","RB50Err")
coeff_predicted[[i]]<-data.frame(NA,NA,NA,NA)
colnames(coeff_predicted[[i]])<-c("SlopeCoef", "Lower_LimitCoef", "Upper_LimitCoef","RB50Coef")
model_pred[[i]]<- as.numeric(fitted(fit))
} #just adding NAs for the times the model failed
}
modelsReps<-data.frame(
do.call(rbind.data.frame,lapply(model_pred,function(x) as.numeric(x))),
Reps_FC$GeneID,
do.call(rbind.data.frame,lapply(pvals,function(x) x) ),
do.call(rbind.data.frame,lapply(coeff_predicted,function(x) x)) ,
do.call(rbind.data.frame,lapply(stderr,function(x) x) )
)
colnames(modelsReps)<-c(pred.names,"GeneID",
"SlopePval", "Lower_LimitPval","Upper_LimitPval", "RB50Pval",
"SlopeCoef", "Lower_LimitCoef","Upper_LimitCoef", "RB50Coef",
"SlopeErr", "Lower_LimitErr","Upper_LimitErr", "RB50Err"
)
data_merged_2 <-merge.data.frame(modelsReps,Reps_FC,by = 'GeneID')
data_merged_2<-data.frame(data_merged_2,"Top_minus_min"=data_merged_2$predX1-data_merged_2[,paste("predX",(input$chans-1),sep = "")])
## crapome integration
crap <- crapome()
#
tempcrap <- crap$Gene
tempcrap<- crap$percentagePresent[match(data_merged_2$GeneID,crap$Gene)]
data_merged_2 <- data.frame(data_merged_2, CRAPomePercent = tempcrap)
proteome<-as.vector(toupper(data_merged_2$GeneID))
mykinases <- intersect(proteome,kinome)
if(!is.null(input$venninp)){
myvenninp <- uploadVenn()
uploadsInt <- intersect(proteome,myvenninp)
myvenvec <- match(proteome, uploadsInt, nomatch = NA)
## now combine with my kin vec
mykinvec <- match(proteome,mykinases, nomatch = NA)
mykinvec[!is.na(mykinvec) & !is.na(myvenvec)] <- 'KINASE + UPLOAD'
mykinvec[!is.na(mykinvec) & is.na(myvenvec)] <- 'KINASE'
mykinvec[is.na(mykinvec) & !is.na(myvenvec)] <- 'UPLOAD'
print(mykinvec)
} else {
mykinvec <- match(proteome,mykinases, nomatch = NA)
mykinvec[!is.na(mykinvec)]<- 'KINASE'
}
data_merged_2<- data.frame(data_merged_2,Kinase = mykinvec)
data_merged_2
}
} else{
conc <- sigConc()
final.Names <- sigFinalNames()
pred.names <- sigPredNames()
colnames(data.merged[,1:input$chans]) <- final.Names
data_merged_positives<- data.merged
# na.omit(data.merged[data.merged[,1:input$chans] >= 1,])
data_merged_positives2<-( (1/data_merged_positives[,1:input$chans]))*100
if(input$incpd == TRUE){
Reps_FC<-data.frame(data_merged_positives2 ,
Accession = data_merged_positives$Accession,GeneID = data_merged_positives$GeneID,
UniquePeps = data_merged_positives$UniquePeps, depletionConstant = data_merged_positives$Kd, MissingVal = data_merged_positives$MissingVal
)
}else{
Reps_FC<-data.frame(data_merged_positives2 ,
Accession = data_merged_positives$Accession,GeneID = data_merged_positives$GeneID,
UniquePeps = data_merged_positives$UniquePeps, MissingVal = data_merged_positives$MissingVal
)
}
ryegrass.m1<- vector(mode = "list",length = nrow(Reps_FC))
pvals<-list()
stderr<-list()
model_pred<-list()
coeff_predicted<-list()
for(i in 1:nrow(Reps_FC)){
#print(i)
#nrow(full_df_2)
#maxIt and relTol to be user defined
ryegrass.m1[[i]]<-try(drm(as.numeric(Reps_FC[i,1:input$chans]) ~ as.numeric(conc),
na.action = na.omit,
control = drmc(constr = FALSE, errorm = FALSE, noMessage = TRUE, maxIt = 1000, relTol = 1e-06),
fct = LL.4(fixed=c(NA, NA, NA, NA), #see note @top this file
names = c("Slope", "Lower Limit", "Upper Limit", "RB50"))),silent = TRUE)
}
failed_sigm=0
for(i in 1:length(ryegrass.m1)){
#print(i)
#checking_val if FALSE the model has failed to calculate the pval
checking_val<-try(is.numeric(coefficients(ryegrass.m1[[i]])[["Slope:(Intercept)"]]),silent = TRUE)
if(checking_val=="TRUE"){
#print(checking_val)
pvals[[i]]<-t(as.data.frame(summary(ryegrass.m1[[i]])$coefficients[13:16]))
colnames(pvals[[i]])<-c("SlopePval", "Lower_LimitPval", "Upper_LimitPval", "RB50Pval")
coeff_predicted[[i]]<-t(data.frame(coefficients(ryegrass.m1[[i]])))
colnames(coeff_predicted[[i]])<-c("SlopeCoef", "Lower_LimitCoef", "Upper_LimitCoef","RB50Coef")
stderr[[i]]<-t(as.data.frame(summary(ryegrass.m1[[i]])$coefficients[5:8]))
colnames(stderr[[i]])<-c("SlopeErr", "Lower_LimitErr", "Upper_LimitErr","RB50Err")
model_pred[[i]]<-predict(ryegrass.m1[[i]])
}else{
failed_sigm=failed_sigm+1
fit <- lm(as.numeric(Reps_FC[i,1:input$chans]) ~ poly(log10(conc),2 ))
#extract the pval
pval<-as.numeric(summary(fit)$coefficients[,4] )
pvals[[i]]<- t(as.data.frame(c(pval,"lm-fit:intercept.slope.quadratic") ))
colnames(pvals[[i]])<-c("SlopePval", "Lower_LimitPval", "Upper_LimitPval","RB50Pval")
stderr[[i]]<- data.frame(NA,NA,NA,NA)
colnames(stderr[[i]])<-c("SlopeErr", "Lower_LimitErr", "Upper_LimitErr","RB50Err")
coeff_predicted[[i]]<-data.frame(NA,NA,NA,NA)
colnames(coeff_predicted[[i]])<-c("SlopeCoef", "Lower_LimitCoef", "Upper_LimitCoef","RB50Coef")
model_pred[[i]]<- as.numeric(fitted(fit))
} #just adding NAs for the times the model failed
}
modelsReps<-data.frame(
do.call(rbind.data.frame,lapply(model_pred,function(x) as.numeric(x))),
Reps_FC$GeneID,
do.call(rbind.data.frame,lapply(pvals,function(x) x) ),
do.call(rbind.data.frame,lapply(coeff_predicted,function(x) x)) ,
do.call(rbind.data.frame,lapply(stderr,function(x) x) )
)
colnames(modelsReps)<-c(pred.names,"GeneID",
"SlopePval", "Lower_LimitPval","Upper_LimitPval", "RB50Pval",
"SlopeCoef", "Lower_LimitCoef","Upper_LimitCoef", "RB50Coef",
"SlopeErr", "Lower_LimitErr","Upper_LimitErr", "RB50Err"
)
data_merged_2<-merge.data.frame(modelsReps,Reps_FC,by="GeneID")
data_merged_2<-data.frame(data_merged_2,"Top_minus_min"=data_merged_2$predX1-data_merged_2[,paste("predX",input$chans,sep = "")])
## crapome integration
crap <- crapome()
#
tempcrap <- crap$Gene
tempcrap<- crap$percentagePresent[match(data_merged_2$GeneID,crap$Gene)]
data_merged_2 <- data.frame(data_merged_2, CRAPomePercent = tempcrap)
proteome<-as.vector(toupper(data_merged_2$GeneID))
mykinases <- intersect(proteome,kinome)
if(!is.null(input$venninp)){
myvenninp <- uploadVenn()
uploadsInt <- intersect(proteome,myvenninp)
myvenvec <- match(proteome, uploadsInt, nomatch = NA)
## now combine with my kin vec
mykinvec <- match(proteome,mykinases, nomatch = NA)
mykinvec[!is.na(mykinvec) & !is.na(myvenvec)] <- 'KINASE + UPLOAD'
mykinvec[!is.na(mykinvec) & is.na(myvenvec)] <- 'KINASE'
mykinvec[is.na(mykinvec) & !is.na(myvenvec)] <- 'UPLOAD'
print(mykinvec)
} else {
mykinvec <- match(proteome,mykinases, nomatch = NA)
mykinvec[!is.na(mykinvec)]<- 'KINASE'
}
if(input$incpd == TRUE){
data_merged_2<- data.frame(data_merged_2, correctedRB50 = (data_merged_2$RB50Coef*data_merged_2$depletionConstant),Kinase = mykinvec)
}else{
data_merged_2<- data.frame(data_merged_2,Kinase = mykinvec)
}
data_merged_2
}
} else{
if(input$datype == "intensity"){
conc<- rep(0:(input$chans - 2), times = input$reps)
}else{
conc<- rep(0:(input$chans - 1), times = rReps())[channels()]
}
design<-model.matrix(~poly(conc,2))
colnames(design)<-c("Intercept","Slope","Quadratic")
# reactive start
fit <- lmFit(data.merged[,1:length(conc)], method = "ls" , design = design )
fit <- eBayes(fit)
res <- topTable(fit, coef = "Slope", number = nrow(data.merged), adjust="BH") #pval for the slope
res2 <- topTable(fit, coef = 1, number = nrow(data.merged), adjust="BH")#pval for the intercept
res3 <- topTable(fit, coef = "Quadratic", number = nrow(data.merged), adjust="BH") #pval for the quadratic term ()
#add the pvalues to the dataframe
tmp_1<- cbind(data.merged[rownames(res),],res)
tmp_2<- cbind(data.merged[rownames(res2),],res2)
tmp_3<- cbind(data.merged[rownames(res3),],res3)
####
tobeselected <- merge.data.frame(tmp_1,tmp_2,by="Accession")
tobeselected <- merge.data.frame(tobeselected,tmp_3,by="Accession")
print(colnames(tobeselected))
selectnames <- c(paste0(colnames(data.merged)[1:length(conc)],".x"),
"logFC.x", "AveExpr.x", "P.Value", "adj.P.Val", "P.Value.x",
"adj.P.Val.x", "P.Value.y", "adj.P.Val.y","Accession","GeneID.x","UniquePeps")
data.merged<- tobeselected[,match(selectnames, colnames(tobeselected))]
print(colnames(data.merged))
proteome<-as.vector(toupper(tobeselected$GeneID.x))
mykinases <- intersect(proteome,kinome)
if(!is.null(input$venninp)){
myvenninp <- uploadVenn()
uploadsInt <- intersect(proteome,myvenninp)
myvenvec <- match(proteome, uploadsInt, nomatch = NA)
## now combine with my kin vec
mykinvec <- match(proteome,mykinases, nomatch = NA)
mykinvec[!is.na(mykinvec) & !is.na(myvenvec)] <- 'KINASE + UPLOAD'
mykinvec[!is.na(mykinvec) & is.na(myvenvec)] <- 'KINASE'
mykinvec[is.na(mykinvec) & !is.na(myvenvec)] <- 'UPLOAD'
print(mykinvec)
} else {
mykinvec <- match(proteome,mykinases, nomatch = NA)
mykinvec[!is.na(mykinvec)]<- 'KINASE'
}
crap <- crapome()
#
tempcrap <- crap$Gene
tempcrap<- crap$percentagePresent[match(toupper(data.merged$GeneID.x),crap$Gene)]
data.merged <- data.frame(data.merged, CRAPomePercent = tempcrap,Kinase = mykinvec)
print(colnames(data.merged))
nam <- finalNames()
if(input$datype == 'intensity'){
nam <- nam[-seq(1,input$reps*input$chans,by = input$chans)]
}
colnames(data.merged)[1:length(nam)] <- nam
# print(colnames(data.merged[match(c('P.Value', 'adj.P.Val', 'P.Value.x', 'adj.P.Val.x', 'P.Value.y', 'adj.P.Val.y'),colnames(data.merged))]))
# colnames(data.merged[,match(c('P.Value', 'adj.P.Val', 'P.Value.x', 'adj.P.Val.x', 'P.Value.y', 'adj.P.Val.y'),colnames(data.merged))]) <- c('P.Value_intercept', 'adj.P.Val_intercept', 'P.Value_slope', 'adj.P.Val_slope', 'P.Value_quadratic', 'adj.P.Val_quadratic')
# colnames(data.merged[match(c('P.Value', 'adj.P.Val', 'P.Value.x', 'adj.P.Val.x', 'P.Value.y', 'adj.P.Val.y'),colnames(data.merged))]) <- c('P.Value_intercept', 'adj.P.Val_intercept', 'P.Value_slope', 'adj.P.Val_slope', 'P.Value_quadratic', 'adj.P.Val_quadratic')
data.merged
}
})
rSu<- reactive({
if(input$reps == 1 ){
data.merged<- dataMerge()
data.merged
}else{
data.merged <- dataMerge2()
data.merged
}
})
###################
## output
###################
output$venn <- renderPlot({
req(data())
if(!is.null(input$venninp)){
upload <- uploadVenn()
upload<- as.vector(toupper(upload))
print(upload)
data.merged <- dataMerge()
proteome<-as.vector(toupper(data.merged$GeneID))
universe <- unique(c(kinome,proteome,upload))
count<- matrix(0, ncol = 3 , nrow = length(universe))
colnames(count) <- c("kinome",'proteome','upload')
for(i in 1:length(universe)){
count[i,1]<- universe[i] %in% kinome
count[i,2]<- universe[i] %in% proteome
count[i,3]<- universe[i] %in% upload
}
vennDiagram(vennCounts(count), circle.col = c("blue","red","green"), cex = 1,lwd = 2)
}else{
data.merged <- dataMerge()
proteome<-as.vector(toupper(data.merged$GeneID))
universe <- unique(c(kinome,proteome))
# Generate a matrix, with the sets in columns and possible letters on rows
Counts <- matrix(0, nrow=length(universe), ncol=2)
# Populate the said matrix
for (i in 1:length(universe)) {
Counts[i,1] <- universe[i] %in% kinome
Counts[i,2] <- universe[i] %in% proteome
#Counts[i,3] <- universe[i] %in% Metacore
#Counts[i,3] <- universe[i] %in% EXOCYTOSIS
}
colnames(Counts) <- c("Kinome","Proteome")
cols<-c("Red", "Blue")
#### VENN
vennDiagram(vennCounts(Counts), circle.col=cols,
cex=1, #title size
lwd=2 #circle line size
)
}
})
output$bar<- renderPlot({
vec<- channels()
vec<- length(vec)
palette.bar <- rep(terrain.colors(input$reps),each = ifelse(input$datype != 'intensity',input$chans,input$chans - 1 ) )
data.merged<- dataMerge()
boxplot(data.merged[,1:vec], col=palette.bar,las=2, cex.axis=1, main=c("Box Plots"),
ylab=c("Log2(ratios)"))
legend("topright",legend = paste("rep",1:input$reps,sep = ' '), fill = terrain.colors(input$reps))
})
output$plot2<-renderPlot({
vec <- channels()
pal <- rainbow(length(vec))
leg.nam <- finalNames()
data.merged <- dataMerge()
missing_val <- 0
par(mfrow = c(1,2))
plot(x=rank(data.merged[,1]),y=data.merged[,1], cex.axis=1,
main=c("Change Distribution"),
col=pal[1], ylab=c("Log2(ratios)"), xlab = c("Proteins"))
if(length(vec) > 1){
for(i in 2:length(vec)){
points(x=rank(data.merged[,i]),y=data.merged[,i], cex.axis=1, main=c(""),col=pal[i])
}
}
legend("topleft", legend = leg.nam, fill = pal)
plot(density(x=data.merged[,1]),col= pal[1], main=c(" Density Distribution"), ylim = c(0,5 ),cex.axis = 1)
legend("topleft", legend = leg.nam, fill = pal)
if(length(vec) > 1){
for(i in 2:length(vec)){
lines(density(x=data.merged[,i]), col=pal[i], main = c(""))
}
}
})
output$plot3<- renderPlot({
vec <- channels()
data.merged<- dataMerge()
# print(colnames(data.merged))
vsn::meanSdPlot(as.matrix(data.merged[,1:length(vec)]))
})
output$plot4<- renderPlot({
if(input$modtyp == 'sigmoid'){
plot.new()
legend('topleft', c("Sigmoidal fit applied, no linear plots available"),bty = 'n')
}else{
data.merged<- dataMerge2()
m0 <- ggplot(data.merged, aes(x=data.merged$P.Value))
m0<-m0 + geom_histogram(aes(fill = ..count..),binwidth = 0.01) +
scale_fill_gradient("Count", low = "green", high = "red")+
xlab("P.val slope")
m1 <- ggplot(data.merged, aes(x=data.merged$P.Value.x))
m1<- m1 + geom_histogram(aes(fill = ..count..),binwidth = 0.01) +
scale_fill_gradient("Count", low = "green", high = "red")+
xlab("Pval intercept")
m2 <- ggplot(data.merged, aes(x=data.merged$P.Value.y))
m2 <- m2 + geom_histogram(aes(fill = ..count..),binwidth = 0.01) +
scale_fill_gradient("Count", low = "green", high = "red")+
xlab("Pval quadratic")
grid.arrange(m0,m1,m2)
}
})
output$volcanoint<- renderPlot({
res<- dataMerge2()
# avgthr=0.2 #sign threshold for the averege fold change 0.3(log2) is 1.3 FC
par(mar=c(5,5,5,10), xpd=TRUE)
# Make a basic volcano plot
with(res, plot(res$AveExpr.x, -log10(res$P.Value.x), pch=20, main="Volcano plot (Intercept pval )",xlab=c("Log2_AvgFC"),ylab=c("-Log10(Pval)"), xlim=c(-abs(max(res$AveExpr.x)+1),abs(max(res$AveExpr.x)+1))))
# Add colored points: red if padj<0.05, orange of log2FC>1, green if both)
s=subset(res, P.Value.x<input$pvalsli )
with(s, points(s$AveExpr.x, -log10(s$P.Value.x), pch=20, col="red"))
s=subset(res, abs(res$AveExpr.x)>input$avthrssli)
with(s, points(s$AveExpr.x, -log10(s$P.Value.x), pch=20, col="orange"))
s=subset(res, P.Value.x<input$pvalsli & abs(res$AveExpr.x)>input$avthrssli)
with(s, points(s$AveExpr.x, -log10(s$P.Value.x), pch=20, col="green"))
# Label points with the textxy function from the calibrate plot
s=subset(res, P.Value.x<input$pvalsli & abs(res$AveExpr.x)>input$avthrssli)
with(s, textxy( s$AveExpr.x, -log10(s$P.Value.x), labs=s$GeneID.x, cex=1)
)
legend("bottomleft", title="Legend",cex = 0.8,
c("Not significant",
paste("P.Value",input$pvalsli, sep = " "), #red
paste("AvgFC >", input$avthrssli, sep=""), #orange,
paste("P.Value", input$pvalsli,"& AvgFC >", input$avthrssli, sep="") #green
),
col=c("black","red","orange","green"),
horiz=FALSE, pch=c(19))
})
output$volcanoquad<- renderPlot({
res<- dataMerge2()
# avgthr=0.2 #sign threshold for the averege fold change 0.3(log2) is 1.3 FC
par(mar=c(5,5,5,10), xpd=TRUE)
# Make a basic volcano plot
with(res, plot(res$AveExpr.x, -log10(res$P.Value.y), pch=20, main="Volcano plot (Quadratic pval )",xlab=c("Log2_AvgFC"),ylab=c("-Log10(Pval)"), xlim=c(-abs(max(res$AveExpr.x)+1),abs(max(res$AveExpr.x)+1))))
# Add colored points: red if padj<0.05, orange of log2FC>1, green if both)
s=subset(res, P.Value.y<input$pvalsli )
with(s, points(s$AveExpr.x, -log10(s$P.Value.y), pch=20, col="red"))
s=subset(res, abs(res$AveExpr.x)>input$avthrssli)
with(s, points(s$AveExpr.x, -log10(s$P.Value.y), pch=20, col="orange"))
s=subset(res, P.Value.y<input$pvalsli & abs(res$AveExpr.x)>input$avthrssli)
with(s, points(s$AveExpr.x, -log10(s$P.Value.y), pch=20, col="green"))
# Label points with the textxy function from the calibrate plot
s=subset(res, P.Value.y<input$pvalsli & abs(res$AveExpr.x)>input$avthrssli)
with(s, textxy( s$AveExpr.x, -log10(s$P.Value.y), labs=s$GeneID.x, cex=.9)
)
legend("bottomleft", title="Legend",cex = 0.7,
c("Not significant",
paste("P.Value",input$pvalsli, sep = " "), #red
paste("AvgFC >", input$avthrssli, sep=""), #orange,
paste("P.Value", input$pvalsli,"& AvgFC >", input$avthrssli, sep="") #green
),
col=c("black","red","orange","green"),
horiz=FALSE, pch=c(19))
})
output$repvsrep1 <- renderUI({
# a <- finalNames()
# a <- paste0(a,".x")
# b <- channels()
a<- indexmatrix()
selectizeInput(inputId = "repvsrep1",label = "Select Condition", choices = as.character(a$names), multiple = FALSE)
})
output$repvsrep2 <- renderUI({
a <- finalNames()
a <- paste0(a,".x")
b <- channels()
c <- a[b]
if(is.null(input$repvsrep1)){
e <- c
} else {
d <- match(input$repvsrep1,c)
e <- c[-d]
}
selectInput(inputId = "repvsrep2",label = "Select Condition", choices = e, multiple = FALSE)
})
output$repvsrep <- renderPlot({
if(input$reps > 1){
data.merged <- dataMerge2()
index <- indexmatrix()
val = max(c(max(data.merged[,index[index[,1] == input$repvsrep1,5]],na.rm = TRUE),max(data.merged[,index[index[,1] == input$repvsrep1,6]],na.rm = TRUE)))
plot(x=data.merged[,index[index[,1] == input$repvsrep1,5]],y=data.merged[,index[index[,1] == input$repvsrep1,6]], xlim=c(0,val +0.2), col="green" , ylim=c(0,val+0.2),
cex.axis=1.2, main=c("LogFC-LogFC Plots"),
xlab=paste("rep",index[index[,1] == input$repvsrep1,3]), ylab=paste("rep",index[index[,1] == input$repvsrep1,4]))
text(data.merged[,index[index[,1] == input$repvsrep1,5]], data.merged[,index[index[,1] == input$repvsrep1,6]], labels=data.merged$GeneID, cex= 1,pos=4)
lines(x = c(0,val), y = c(0,val),col="red")
} else {
plot.new()
title(main = 'Plot not available: only 1 replicate')
}
})
output$plot5<- renderPlot({
req(data())
if(input$modtyp == 'sigmoid'){
su <- dataMerge()
}else{
su<- rSu()
}
index<- channels()
index<- length(index)
cmat <-cor(su[,1:index],use="pairwise", method = "pearson")
corrgram(cmat, order=TRUE, lower.panel=panel.shadeNtext,
upper.panel=panel.pie, text.panel=panel.txt,
main="Corrgram Plots" )
})
### MeanDiff
output$meandiff1 <- renderUI({
a <- indexmatrix()
selectizeInput(inputId = "meandiff1",label = "Select Condition", choices = as.character(a$names), multiple = FALSE)
})
output$meandiff2 <- renderUI({
a <- finalNames()
a <- paste0(a,".x")
b <- channels()
c <- a[b]
if(is.null(input$meandiff1)){
e <- c
} else {
d <- match(input$meandiff1,c)
e <- c[-d]
}
selectInput(inputId = "meandiff2",label = "Select Condition", choices = e, multiple = FALSE)
})
output$plot6<- renderPlot({
req(data())
if(input$modtyp == 'sigmoid' | input$reps == 1){
plot.new()
title(main = 'Plot not available: only 1 replicate')
}else{
# data.merged <- dataMerge()
su <- rSu()
index <- indexmatrix()
minxy <- min(c(min(su[,index[index[,1] == input$meandiff1,5]]),min(su[,index[index[,1] == input$meandiff1,6]])))
maxxy <- max(c(max(su[,index[index[,1] == input$meandiff1,5]]),max(su[,index[index[,1] == input$meandiff1,6]])))
tmd(
xyplot(su[,index[index[,1] == input$meandiff1,5]] ~ su[,index[index[,1] == input$meandiff1,6]]), main=input$meandiff1,xlim = c(minxy,maxxy),
ylim = c(minxy,maxxy),
panel=function(x, y, ...) {
panel.xyplot(x, y, ...);
ltext(x=x, y=y, labels=su$GeneID, pch=c(13,3,16), cex=0.5, lwd=2, pos=1, offset=1, pch = 19)
}
)
}
})
output$plot7<- renderPlot({
req(data())
if( input$datype == 'intensity'){
nchan<- input$chans - 1
}else{
nchan<- input$chans
}
su <- rSu()
reps <- input$reps
index <- channels()
print(.libPaths())
print(all.equal(1:nchan,index))
print(input$reps)
pca <- prcomp(su[,1:length(index)], scale=FALSE)
DTA<-data.frame( as.numeric(t(su[,1:length(index)])%*%pca$x[,1]),
as.numeric(t(su[,1:length(index)])%*%pca$x[,2]))
print(DTA)
p<-ggplot(DTA, aes(x=DTA$as.numeric.t.su...1.length.index........pca.x...1..,
y=DTA$as.numeric.t.su...1.length.index........pca.x...2..))
paste0("PC1", " (", round(pca$sdev[1]/sum(pca$sdev)*100,0), "%)")
shapeval <- c(15:18,7:12)
p <- p + geom_point(aes(colour = factor(rep(1:print(input$reps),each = (nchan)),labels = paste("Rep",1:print(input$reps)))[index],
shape = factor(rep(1:nchan,print(input$reps)),labels = c(paste("C",0:(nchan-1),sep = "")))[index] ), size = 5 ) +
scale_shape_manual(values=shapeval[1:nchan]) + labs(x = paste0("PC1", " (", round(pca$sdev[1]/sum(pca$sdev)*100,0), "%)"),
y = paste0("PC2", " (", round(pca$sdev[2]/sum(pca$sdev)*100,0), "%)"), title="PCA") + labs(color = "Replicates", shape="Concentration")
print(p)
})
output$plot8<- renderPlot({
if( input$modtyp == 'sigmoid'){
plot.new()
title(main = 'Plot not available: Sigmoidal fit applied')
}else{
res<- dataMerge2()
# avgthr=0.2 #sign threshold for the averege fold change 0.3(log2) is 1.3 FC
par(mar=c(5,5,5,10), xpd=TRUE)
# Make a basic volcano plot
with(res, plot(res$AveExpr.x, -log10(res$P.Value), pch=20, main="Volcano plot (slope pval )",
xlab=c("Log2_AvgFC"),ylab=c("-Log10(Pval)"),
xlim=c(-abs(max(res$AveExpr.x)+1),abs(max(res$AveExpr.x)+1))))
# Add colored points: red if padj<0.05, orange of log2FC>1, green if both)
s=subset(res, P.Value< input$pvalsli )
with(s, points(s$AveExpr.x, -log10(s$P.Value), pch=20, col="red"))
s=subset(res, abs(res$AveExpr.x)>input$avthrssli)
with(s, points(s$AveExpr.x, -log10(s$P.Value), pch=20, col="orange"))
s=subset(res, P.Value< input$pvalsli & abs(res$AveExpr.x)>input$avthrssli)
with(s, points(s$AveExpr.x, -log10(s$P.Value), pch=20, col="green"))
# Label points with the textxy function from the calibrate plot
s=subset(res, P.Value< input$pvalsli & abs(res$AveExpr.x)>input$avthrssli)
with(s, textxy( s$AveExpr.x, -log10(s$P.Value), labs=s$GeneID, cex=1)
)
legend("bottomleft", title="Legend",cex = 0.7,
c("Not significant",
paste("P.Value",input$pvalsli, sep = " "), #red
paste("AvgFC >", input$avthrssli, sep=""), #orange,
paste("P.Value", input$pvalsli,"& AvgFC >", input$avthrssli, sep="") #green
),
col=c("black","red","orange","green"),
horiz=FALSE, pch=c(19))
}
})
output$plot9<- renderPlot({
req(data())
if(input$modtyp == 'sigmoid'){
su <- dataMerge()
print(head(su))
if(input$datype =='intensity'){
su1 <- su[,1:(input$chans - 1 )]
}else{
su1 <- su[,1:(input$chans )]
}
} else {
su <- rSu()
vec <- channels()
vec <- length(vec)
su1 <- su[,1:(vec)]
vec.nam <- finalNames()
vec.nam <- vec.nam[channels()]
colnames(su)[match('GeneID.x',colnames(su))] <- 'GeneID'
}
plot.new()
#d3heatmap(su1, Colv = FALSE,labRow = as.character(make.names(su$GeneID,unique = TRUE)), dendrogram = 'row' )
})
output$test<- DT::renderDataTable({
fin<- standardNames()
if(length(input$view_vars) == length(fin)){
DT::datatable(data.frame(Original = input$view_vars,Standard = standardNames(), Final = finalNames()))
}else{
DT::datatable(data.frame(Error = "Incorrect dimensions", Comments= "ensure the number of names selected is the same as the number of channels and repeats inputted"))
}
})
############## Info Boxes
### P value
pvalQc <- reactive({
data.merged <- dataMerge2()
PVal <- c(sum(data.merged$P.Value <= 0.05),sum(data.merged$P.Value.x <= 0.05),
sum(data.merged$P.Value.y <= 0.05))
Names = c("Slope", "Intercept", "Quadratic")
data.frame(Names = Names, PVal = PVal)
})
output$infopvalslo <- renderInfoBox({
temp <- pvalQc()
infoBox(
title = "Slope",paste0(temp[1,2], " p values < 0.05"),color = ifelse(temp[1,2] > 0, "green","orange" ), icon = icon(ifelse(temp[1,2] > 0, "check","warning" ))
)
})
output$infopvalint <- renderInfoBox({
temp <- pvalQc()
infoBox(
title = "Intercept",paste0(temp[2,2], " p values < 0.05"),color = ifelse(temp[2,2] > 0, "green","orange" ), icon = icon(ifelse(temp[2,2] > 0, "check","warning" ))
)
})
output$infopvalquad <- renderInfoBox({
temp <- pvalQc()
infoBox(
title = "Quadratic",paste0(temp[3,2], " p values < 0.05"),color = ifelse(temp[3,2] > 0, "green","orange" ), icon = icon(ifelse(temp[2,2] > 0, "check","warning" ))
)
})
output$corrinfo <- renderInfoBox({
req(data())
if(input$modtyp == 'sigmoid'){
su <- dataMerge()
}else{
su <- rSu()
}
cmat <-cor(su[,channels()],use="pairwise", method = "pearson")
cmat[upper.tri(cmat)]<- 0
cmat<- melt(cmat)
infoBox(
title = NULL,value = ifelse(nrow(cmat[cmat$value < 0, ]) == 0, "No Anti-Correlation between Channels","Anti Correlation between some Channels" ),
color = ifelse(nrow(cmat[cmat$value < 0, ]) == 0, "green","orange" ),
icon = icon(ifelse(nrow(cmat[cmat$value < 0, ]) == 0, "check","warning" ))
)
})
output$siginfodt <- renderInfoBox({
if(input$modtyp == 'lin'){
return(NULL)
} else {
conc<- sigConc()
if(input$datype == 'intensity'){
top<-15 #max prot to plot
data_merged_2 <- dataMerge2()
# RB50<-na.omit(data_merged_2[data_merged_2$RB50Err < as.numeric(summary(data_merged_2$RB50Err)[5]) & data_merged_2$RB50Pval<0.05 & data_merged_2$predX1-data_merged_2$predX9 >0 & data_merged_2$predX1 <= 100,])
RB50 <- data.frame(na.omit(data_merged_2[data_merged_2$RB50Err < as.numeric(summary(data_merged_2$RB50Err)[5]) & data_merged_2$RB50Pval < 0.05
& data_merged_2$predX1-data_merged_2[,paste("predX",(input$chans - 1),sep = "")] >0 & data_merged_2$predX1 <= 100,]))
RB50_ordered<- na.omit(RB50[order(RB50$RB50Pval, decreasing = FALSE),][1:top,])
} else{
pred.names <- sigPredNames()
final.Names <- finalNames()
top<-15 #max prot to plot
data_merged_2 <- dataMerge2()
# RB50<-na.omit(data_merged_2[data_merged_2$RB50Err < as.numeric(summary(data_merged_2$RB50Err)[5]) & data_merged_2$RB50Pval<0.05 & data_merged_2$predX1-data_merged_2$predX9 >0 & data_merged_2$predX1 <= 100,])
RB50 <- data.frame(na.omit(data_merged_2[data_merged_2$RB50Err < as.numeric(summary(data_merged_2$RB50Err)[5]) & data_merged_2$RB50Pval < 0.05
& data_merged_2$predX1-data_merged_2[,paste("predX",input$chans,sep = "")] >0 & data_merged_2$predX1 <= 100,]))
RB50_ordered<- na.omit(RB50[order(RB50$RB50Pval, decreasing = FALSE),][1:top,])
}
infoBox(
title = "RB50",paste0(nrow(RB50_ordered), " Significant RB50"),color = ifelse(nrow(RB50_ordered) > 0, "green","orange" ), icon = icon(ifelse(nrow(RB50_ordered) > 0, "check","warning" ))
)
}
})
output$siginfoslop <- renderInfoBox({
if(input$modtyp == 'lin'){
return(NULL)
} else {
conc<- sigConc()
if(input$datype == 'intensity'){
top<-15 #max prot to plot
conc<- sigConc()
pred.names <- paste0('predX',1:(input$chans -1))
final.Names <- paste0('rep1_C',0:(input$chans - 2))
data_merged_2 <- dataMerge2()
#Here make the subselections for using the ggplot functions SLOPE
slope<-na.omit(data_merged_2[data_merged_2$SlopePval<0.05 ,])
slope_ordered<-na.omit(slope[order(slope$SlopePval, decreasing = FALSE),][1:top,])
} else{
top<-15 #max prot to plot
conc<- sigConc()
pred.names <- sigPredNames()
final.Names <- finalNames()
data_merged_2 <- dataMerge2()
#Here make the subselections for using the ggplot functions SLOPE
slope<-na.omit(data_merged_2[data_merged_2$SlopePval<0.05 ,])
slope_ordered<-na.omit(slope[order(slope$SlopePval, decreasing = FALSE),][1:top,])
}
infoBox(
title = "Slope Coefficient",paste0(nrow(slope_ordered), " Significant Slope"),color = ifelse(nrow(slope_ordered) > 0, "green","orange" ), icon = icon(ifelse(nrow(slope_ordered) > 0, "check","warning" ))
)
}
})
output$siginfodiff <- renderInfoBox({
if(input$modtyp == 'lin'){
return(NULL)
} else {
conc<- sigConc()
if(input$datype == 'intensity'){
data_merged_2 <- dataMerge2()
pred.names <- paste0('predX',1:(input$chans -1))
final.Names <- paste0('rep1_C',0:(input$chans - 2))
topperc<-30 #difference in % between top and bottom
# data_merged_2 <- dataMerge2()
diffinter<- data_merged_2[(data_merged_2$predX1 -data_merged_2[,paste("predX",(input$chans-1),sep = "")]) > topperc & data_merged_2$predX1 <= 100, ]
} else{
conc<- sigConc()
pred.names <- sigPredNames()
final.Names <- finalNames()
topperc<-30 #difference in % between top and bottom
data_merged_2 <- dataMerge2()
diffinter<- data_merged_2[(data_merged_2$predX1 -data_merged_2[,paste("predX",input$chans,sep = "")]) > topperc & data_merged_2$predX1 <= 100, ]
}
infoBox(
title = "Top - Bottom Difference",paste0(nrow(diffinter), " Significant Difference"),color = ifelse(nrow(diffinter) > 0, "green","orange" ), icon = icon(ifelse(nrow(diffinter) > 0, "check","warning" ))
)
}
})
############################
# SIGMOIDAL PLOTS
############################
output$DiffTopBottom <- renderPlot({
if(input$modtyp != 'sigmoid'){
plot.new()
legend('topleft', c("Linear fit applied, no sigmoidal plots available"),bty = 'n')
}else{
if(input$datype == 'intensity'){
data_merged_2 <- dataMerge2()
conc<- sigConc()
pred.names <- paste0('predX',1:(input$chans -1))
final.Names <- paste0('rep1_C',0:(input$chans - 2))
topperc<-30 #difference in % between top and bottom
# data_merged_2 <- dataMerge2()
diffinter<- data_merged_2[(data_merged_2$predX1 -data_merged_2[,paste("predX",(input$chans-1),sep = "")]) > topperc & data_merged_2$predX1 <= 100, ]
if(nrow(diffinter)>0){
Diff_Top_bottom_pred<-shape_for_ggplot_pred(diffinter,log2(conc),pred.names)
Diff_Top_bottom_perc<-shape_for_ggplot_perc(diffinter,log2(conc),final.Names)
what<-c("(Top - Bottom) >")
Diff_Top_bottom<-ggplot()+
geom_line(data = Diff_Top_bottom_pred, aes(x=x,y=value, colour=factor(Diff_Top_bottom_pred$GeneID)), size = 1) +
geom_point(data = Diff_Top_bottom_perc, aes(x=x,y=value, colour=Diff_Top_bottom_perc$GeneID)) +
labs(title=paste(what,topperc,sep=""))
}else{
Diff_Top_bottom<-ggplot()+
labs(title=paste("No significant Top-Bottom >" ,topperc,"%","\n","has been found", sep=""))
}
print(Diff_Top_bottom)
}
else{
conc<- sigConc()
pred.names <- sigPredNames()
final.Names <- finalNames()
topperc<-30 #difference in % between top and bottom
data_merged_2 <- dataMerge2()
diffinter<- data_merged_2[(data_merged_2$predX1 -data_merged_2[,paste("predX",input$chans,sep = "")]) > topperc & data_merged_2$predX1 <= 100, ]
if(nrow(diffinter)>0){
Diff_Top_bottom_pred<-shape_for_ggplot_pred(diffinter,log2(conc),pred.names)
Diff_Top_bottom_perc<-shape_for_ggplot_perc(diffinter,log2(conc),final.Names)
what<-c("(Top - Bottom) >")
Diff_Top_bottom<-ggplot()+
geom_line(data = Diff_Top_bottom_pred, aes(x=x,y=value, colour=factor(Diff_Top_bottom_pred$GeneID)), size = 1) +
geom_point(data = Diff_Top_bottom_perc, aes(x=x,y=value, colour=Diff_Top_bottom_perc$GeneID)) +
labs(title=paste(what,topperc,sep=""))
}else{
Diff_Top_bottom<-ggplot()+
labs(title=paste("No significant Top-Bottom >" ,topperc,"%","\n","has been found", sep=""))
}
print(Diff_Top_bottom)
}
}
})
output$Slope_pl <- renderPlot({
if(input$modtyp != 'sigmoid'){
plot.new()
legend('topleft', c("Linear fit applied, no sigmoidal plots available"),bty = 'n')
}else{
if(input$datype == 'intensity'){
top<-15 #max prot to plot
conc<- sigConc()
pred.names <- paste0('predX',1:(input$chans -1))
final.Names <- paste0('rep1_C',0:(input$chans - 2))
data_merged_2 <- dataMerge2()
#Here make the subselections for using the ggplot functions SLOPE
slope<-na.omit(data_merged_2[data_merged_2$SlopePval<0.05 ,])
slope_ordered<-na.omit(slope[order(slope$SlopePval, decreasing = FALSE),][1:top,])
if(nrow(slope_ordered)>0){
slope_pred<-shape_for_ggplot_pred(slope_ordered,log10(conc),pred.names)
slope_perc<- shape_for_ggplot_perc(slope_ordered,log10(conc),final.Names)
what<-c("Slope (p.val) ")
Slope_pl<-ggplot()+
geom_line(data = slope_pred, aes(x=x,y=value, colour=factor(slope_pred$GeneID)), size = 1) +
geom_point(data = slope_perc, aes(x=x,y=value,colour=slope_perc$GeneID))+
labs(title=paste(what,"Top",top,sep=""))
}else{Slope_pl<-ggplot()+
labs(title="No significant Sigmoidal Slope has been found")
}
print(Slope_pl)
} else{
top<-15 #max prot to plot
conc<- sigConc()
pred.names <- sigPredNames()
final.Names <- finalNames()
data_merged_2 <- dataMerge2()
#Here make the subselections for using the ggplot functions SLOPE
slope<-na.omit(data_merged_2[data_merged_2$SlopePval<0.05 ,])
slope_ordered<-na.omit(slope[order(slope$SlopePval, decreasing = FALSE),][1:top,])
if(nrow(slope_ordered)>0){
slope_pred<-shape_for_ggplot_pred(slope_ordered,log10(conc),pred.names)
slope_perc<- shape_for_ggplot_perc(slope_ordered,log10(conc),final.Names)
what<-c("Slope (p.val) ")
Slope_pl<-ggplot()+
geom_line(data = slope_pred, aes(x=x,y=value, colour=factor(slope_pred$GeneID)), size = 1) +
geom_point(data = slope_perc, aes(x=x,y=value,colour=slope_perc$GeneID))+
labs(title=paste(what,"Top",top,sep=""))
}else{Slope_pl<-ggplot()+
labs(title="No significant Sigmoidal Slope has been found")
}
print(Slope_pl)
}
}
})
output$RB50 <- renderPlot({
if(input$modtyp != 'sigmoid'){
plot.new()
legend('topleft', c("Linear fit applied, no sigmoidal plots available"),bty = 'n')
}else{
if(input$datype =='intensity'){
conc<- sigConc()
pred.names <- paste0('predX',1:(input$chans -1))
final.Names <- paste0('rep1_C',0:(input$chans - 2))
top<-15 #max prot to plot
data_merged_2 <- dataMerge2()
# RB50<-na.omit(data_merged_2[data_merged_2$RB50Err < as.numeric(summary(data_merged_2$RB50Err)[5]) & data_merged_2$RB50Pval<0.05 & data_merged_2$predX1-data_merged_2$predX9 >0 & data_merged_2$predX1 <= 100,])
RB50 <- data.frame(na.omit(data_merged_2[data_merged_2$RB50Err < as.numeric(summary(data_merged_2$RB50Err)[5]) & data_merged_2$RB50Pval < 0.05
& data_merged_2$predX1-data_merged_2[,paste0('predX',(input$chans - 1))] >0 & data_merged_2$predX1 <= 100,]))
RB50_ordered<- na.omit(RB50[order(RB50$RB50Pval, decreasing = FALSE),][1:top,])
if(nrow(RB50_ordered)>0){
RB50_pred<-shape_for_ggplot_pred(RB50_ordered,log10(conc),pred.names)
RB50_perc<-shape_for_ggplot_perc(RB50_ordered,log10(conc),final.Names)
what<-c("RB50 (p.val) ")
RB50_pl<-ggplot()+
geom_line(data = RB50_pred, aes(x=x,y=value, colour=factor(RB50_pred$GeneID)), size = 1) +
geom_point(data = RB50_perc, aes(x=x,y=value,colour=RB50_perc$GeneID))+
labs(title=paste(what,"Top",top,sep=""))
print(RB50_pl)
}else{
RB50_pl<-ggplot()+
labs(title="No significant RB50 has been found")
print(RB50_pl)
}
}else {
conc<- sigConc()
pred.names <- sigPredNames()
final.Names <- finalNames()
top<-15 #max prot to plot
data_merged_2 <- dataMerge2()
# RB50<-na.omit(data_merged_2[data_merged_2$RB50Err < as.numeric(summary(data_merged_2$RB50Err)[5]) & data_merged_2$RB50Pval<0.05 & data_merged_2$predX1-data_merged_2$predX9 >0 & data_merged_2$predX1 <= 100,])
RB50 <- data.frame(na.omit(data_merged_2[data_merged_2$RB50Err < as.numeric(summary(data_merged_2$RB50Err)[5]) & data_merged_2$RB50Pval < 0.05
& data_merged_2$predX1-data_merged_2$predX9 >0 & data_merged_2$predX1 <= 100,]))
RB50_ordered<- na.omit(RB50[order(RB50$RB50Pval, decreasing = FALSE),][1:top,])
if(nrow(RB50_ordered)>0){
RB50_pred<-shape_for_ggplot_pred(RB50_ordered,log10(conc),pred.names)
RB50_perc<-shape_for_ggplot_perc(RB50_ordered,log10(conc),final.Names)
what<-c("RB50 (p.val) ")
RB50_pl<-ggplot()+
geom_line(data = RB50_pred, aes(x=x,y=value, colour=factor(RB50_pred$GeneID)), size = 1) +
geom_point(data = RB50_perc, aes(x=x,y=value,colour=RB50_perc$GeneID))+
labs(title=paste(what,"Top",top,sep=""))
}else{
RB50_pl<-ggplot()+
labs(title="No significant RB50 has been found")
}
print(RB50_pl)
}
}
})
# Linear elements of sigmoidal obselete
# output$Linear_pl1 <- renderPlot({
#
# if(input$modtyp != 'sigmoid'){
# plot.new()
# legend('topleft', c("Linear fit applied, no sigmoidal plots available"),bty = 'n')
# }else{
# conc<- sigConc()
#
# pred.names <- sigPredNames()
# final.Names <- finalNames()
# top<-15 #max prot to plot
#
# data_merged_2 <- dataMerge2()
#
#
# linere<-data_merged_2[data_merged_2$RB50Pval=="lm-fit:intercept.slope.quadratic" & data_merged_2$predX1 > data_merged_2[,paste("predX",input$chans,sep = "")] & data_merged_2$predX1 <= 100 & data_merged_2$Lower_LimitPval < 0.05,]
#
# if(nrow(linere)>0){
# lin_pred<-shape_for_ggplot_pred(linere,log10(conc),pred.names)
# lin_perc<-shape_for_ggplot_perc(linere,log10(conc),final.Names)
# what<-c("Lm model Slope Pval< 0.05 \n (failed dose-resp.) ")
#
# Linear_pl1<-ggplot()+
# geom_line(data = lin_pred, aes(x=x,y=value, colour=factor(lin_pred$GeneID)), size = 1) +
# geom_point(data = lin_perc, aes(x=x,y=value,colour=lin_perc$GeneID))+
# labs(title=paste(what,top,sep=""))
#
#
# }else{
# Linear_pl1<-ggplot()+
# labs(title="No significant Lm slope has been found")
# }
#
# print(Linear_pl1)
# }
# })
#
# output$Linear_pl2 <- renderPlot({
#
# if(input$modtyp != 'sigmoid'){
# plot.new()
# legend('topleft', c("Linear fit applied, no sigmoidal plots available"),bty = 'n')
# }else{
# conc<- sigConc()
# pred.names <- sigPredNames()
# final.Names <- finalNames()
# top<-15 #max prot to plot
#
# data_merged_2 <- dataMerge2()
#
#
# linere<-data_merged_2[data_merged_2$RB50Pval=="lm-fit:intercept.slope.quadratic" & data_merged_2$predX1 > data_merged_2[,paste("predX",input$chans,sep = "")] & data_merged_2$predX1 <= 100 & data_merged_2$Upper_LimitPval < 0.05,]
#
# if(nrow(linere)>0){
# lin_pred<-shape_for_ggplot_pred(linere,log10(conc),pred.names)
# lin_perc<-shape_for_ggplot_perc(linere,log10(conc),final.Names)
# what<-c("Lm model Quadratic Pval< 0.05 \n (failed dose-resp.) ")
#
# Linear_pl2<-ggplot()+
# geom_line(data = lin_pred, aes(x=x,y=value, colour=factor(lin_pred$GeneID)), size = 1) +
# geom_point(data = lin_perc, aes(x=x,y=value,colour=lin_perc$GeneID))+
# labs(title=paste(what,top,sep=""))
#
#
# }else{
# Linear_pl2<-ggplot()+
# labs(title="No significant Lm Quadratic has been found")
# }
#
#
# print(Linear_pl2)
# }
#
# })
#
output$testmerge <- DT::renderDataTable({
# a<- intData()
a<- dataMerge2()
# a <- indexmatrix()
# a <- rSu()
if(input$modtyp == 'sigmoid'){
if(input$incpd == TRUE){
DT::datatable(data.frame(GeneID = a$GeneID, RB50 = a$RB50Coef, RB50pval = a$RB50Pval,Topminusbottom = a$Top_minus_min ,correctedRB50 = a$correctedRB50, depletionConst = a$depletionConstant, Kinase = a$Kinase),
options = list(scrollX = TRUE) )
}else{
DT::datatable(data.frame(GeneID = a$GeneID, RB50 = a$RB50Coef, RB50pval = a$RB50Pval,Topminusbottom = a$Top_minus_min , Kinase = a$Kinase),
options = list(scrollX = TRUE) )
}
} else{
DT::datatable(data.frame(GeneID = a$GeneID.x, Intercept = signif(a$P.Value), Slope = signif(a$P.Value.x), Quadtratic = signif(a$P.Value.y), Kinase = a$Kinase),
options = list(scrollX = TRUE) )
}
})
output$kintab <- DT::renderDataTable({
data.merged <- dataMerge()
proteome<-as.vector(toupper(data.merged$GeneID))
DT::datatable(data.frame(GeneID = intersect(proteome,kinome)))
}
)
#################
## OUTPUT download
#################
output$peprmv<- downloadHandler(
filename = function() {
paste("removedPep", '.csv', sep='')
},
content = function(file) {
write.csv(pepdwn(), file)
}
)
output$report <- downloadHandler(
# For PDF output, change this to "report.pdf"
filename = "report.html",
content = function(file) {
# Copy the report file to a temporary directory before processing it, in
# case we don't have write permissions to the current working dir (which
# can happen when deployed).
tempReport <- file.path(tempdir(), "report.Rmd")
file.copy("report.Rmd", tempReport, overwrite = TRUE)
# Set up parameters to pass to Rmd document
params <- list(chans = input$chans, reps = input$reps, data = dataMerge(), data2 = dataMerge2(), channel = channels(), avthrsli = input$avthrssli,
pvalsli = input$pvalsli, indexmat = indexmatrix(), RSu = rSu(), finNam = finalNames(), datype = input$datype, sigmodin = input$modtyp, concen = sigConc(), sigPred = sigPredNames()
,
vennip = input$venninput, kin = kinome1
# , upVenn <- uploadVenn()
)
# Knit the document, passing in the `params` list, and eval it in a
# child of the global environment (this isolates the code in the document
# from the code in this app).
rmarkdown::render(tempReport, output_file = file,
params = params,
envir = new.env(parent = globalenv())
)
}
)
DownloadData<- reactive({
data.merged <- dataMerge2()
if(input$modtyp != 'sigmoid'){
colnames(data.merged)[match(c('P.Value', 'adj.P.Val', 'P.Value.x', 'adj.P.Val.x', 'P.Value.y', 'adj.P.Val.y'),colnames(data.merged))] <- c( 'P.Value_slope', 'adj.P.Val_slope', 'P.Value_intercept', 'adj.P.Val_intercept','P.Value_quadratic', 'adj.P.Val_quadratic')
}
print(head(data.merged))
data.merged
})
output$downloadData <- downloadHandler(
filename = function() {
paste(input$dataset, '.csv', sep='')
},
content = function(file) {
write.csv(DownloadData(), file)
}
)
## rest elements -- doesn't get rendered
output$testkd<- DT::renderDataTable({
# kd<- rKd()
#
# DT::datatable(data.frame(kd))
# a<- dataMerge2()
# a<- rSu()
# a<- uniprotGene()
a<- DownloadData()
DT::datatable(a,
options = list(scrollX = TRUE) )
})
output$sessionInfo <- renderPrint({
capture.output(sessionInfo())
})
})
# Run the application
shinyApp(ui = ui, server = server)
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# https://bruniec.shinyapps.io/doscheda/
library(hexbin)
library(MASS)
library(shiny)
library(shinydashboard)
library(stringr)
library(affy)
library(limma)
library(DT)
library(ggplot2)
library(vsn)
library(gridExtra)
library(lattice)
library(corrgram)
library(calibrate)
library(reshape2)
library(readxl)
library(MASS)
library(lazyeval)
library(drc)
library(httr)
library(jsonlite)
library(rmarkdown)
library(dplyr)
library(prodlim)
################### Load Function
loadingLogo <- function( src, loadingsrc, height = NULL, width = NULL, alt = NULL) {
tagList(
tags$head(
tags$script(
"setInterval(function(){
if ($('html').attr('class')=='shiny-busy') {
$('div.busy').show();
$('div.notbusy').hide();
} else {
$('div.busy').hide();
$('div.notbusy').show();
}
},100)")
),
tags$a(
div(class = "busy",
img(src=loadingsrc,height = height, width = width, alt = alt)),
div(class = 'notbusy',
img(src = src, height = height, width = width, alt = alt))
)
)
}
# plotting functions for sigmoidal
shape_for_ggplot_pred<-function(df_ordered,conc,pred.names){
cols_to_keep_pred<-c(pred.names,"GeneID","Accession")
forggplot_pred<-vector(mode = "list",length = length(df_ordered$GeneID))
for(i in 1:length(df_ordered$GeneID)){
tmp_pred<-df_ordered[,cols_to_keep_pred]
forggplot_pred[[i]]<-melt(tmp_pred[i,], id = c("GeneID", "Accession"), na.rm = TRUE)
}
forggplot_pred_1<-do.call(rbind, forggplot_pred)
forggplot_pred_1<-data.frame(forggplot_pred_1,"x"=conc)
#return(forggplot_pred_1)
}
shape_for_ggplot_perc<-function(df_ordered,conc,finalNames){
cols_to_keep_perc<-c(finalNames, "GeneID","Accession")
forggplot_perc<- vector(mode = "list",length = length(df_ordered$GeneID))
for(i in 1:length(df_ordered$GeneID)){
tmp_perc<-df_ordered[,cols_to_keep_perc]
forggplot_perc[[i]]<-melt(tmp_perc[i,], id = c("GeneID", "Accession"), na.rm = TRUE)
}
forggplot_perc_1<-do.call(rbind, forggplot_perc)
forggplot_perc_1<-data.frame(forggplot_perc_1,"x"=conc)
#return(forggplot_perc_1)
}
pie_chart <- function(df, main, labels = NULL, condition = NULL) {
# convert the data into percentages. group by conditional variable if needed
df <- group_by_(df, .dots = c(condition, main)) %>%
summarise(counts = n()) %>%
mutate(perc = counts / sum(counts)) %>%
arrange(desc(perc)) %>%
mutate(label_pos = cumsum(perc) - perc / 2,
perc_text = paste0(round(perc * 100), "%", "\n","(",counts, ")"))
# reorder the category factor levels to order the legend
df[[main]] <- factor(df[[main]], levels = unique(df[[main]]))
# if labels haven't been specified, use what's already there
if (is.null(labels)) labels <- as.character(df[[main]])
p <- ggplot(data = df, aes_string(x = factor(1), y = "perc", fill = main)) +
# make stacked bar chart with black border
geom_bar(stat = "identity", color = "black", width = 1) +
# add the percents to the interior of the chart
geom_text(aes(x = 1.25, y = label_pos, label = perc_text), size = 4) +
# add the category labels to the chart
# increase x / play with label strings if labels aren't pretty
geom_text(aes(x = 1.82, y = label_pos, label = labels), size = 4) +
# convert to polar coordinates
coord_polar(theta = "y") +
# formatting
scale_y_continuous(breaks = NULL) +
scale_fill_discrete(name = "", labels = unique(labels)) +
theme(text = element_text(size = 12),
axis.ticks = element_blank(),
axis.text = element_blank(),
axis.title = element_blank())
# facet wrap if that's happening
if (!is.null(condition)) p <- p + facet_wrap(condition)
return(p)
}
##upload kinase file
kinome1<-read.csv(file="KinaseFile.csv", header=TRUE, sep=",")
kinome<-as.vector(toupper(kinome1$new.Symbol))
logvc<- function(x) sqrt(exp(x*log(2))^2 - 1 )
# Peptide matching function
peptide.match<- function(dr1,dr2,nchan){
maxrow <- max(nrow(dr1),nrow(dr2))
minrow <- min(nrow(dr1),nrow(dr2))
adVal <- maxrow - minrow
if(nrow(dr1) == maxrow){
dr2$addedVals <- adVal
big.pep <- dr1
small.pep <- dr2
} else {
dr1$addedVals <- adVal
big.pep <- dr2
small.pep <- dr1
}
newframe <- big.pep
colnames(newframe) <- colnames(small.pep)
newframe[1:minrow,] <- small.pep
for(i in 1:nchan){
newframe[(minrow+1):maxrow,i]<- mean(small.pep[,i])
}
if (all.equal(dim(big.pep),dim(dr1)) == TRUE){
dr2 <- newframe
} else {
dr1 <- newframe
}
list(dr1 = dr1, dr2 = dr2 )
}
panel.shadeNtext <- function (x, y, corr = NULL, col.regions, ...)
{
if (is.null(corr))
corr <- cor(x, y, use = "
pair")
ncol <- 14
pal <- col.regions(ncol)
col.ind <- as.numeric(cut(corr, breaks = seq(from = -1, to = 1,
length = ncol + 1), include.lowest = TRUE))
usr <- par("usr")
rect(usr[1], usr[3], usr[2], usr[4], col = pal[col.ind],
border = NA)
box(col = "lightgray")
on.exit(par(usr))
par(usr = c(0, 1, 0, 1))
r <- formatC(corr, digits = 2, format = "f")
cex.cor <- .8/strwidth("-X.xx")
text(0.5, 0.5, r, cex = cex.cor)
}
#########################################################################
## UI
#########################################################################
ui <- shinyUI(dashboardPage(
dashboardHeader(title = loadingLogo('titleogo.png','logogifopt.gif',height = 55,width = 165)),
dashboardSidebar(
sidebarMenu(id = "menu1",
menuItem(text = "Introduction", tabName = "intro"),
#menuItem(text = "Step by Step Guide", tabName = 'stbyst'),
conditionalPanel(
condition = "input.menu1 == 'stbyst'",
radioButtons(inputId = "stage",label = NULL, choices =
c("Stage 1: Data Upload" = "stage1",
"Stage 2: Navigating Plots" = "stage2",
"Stage 3: Download Results" = "stage3"))
),
menuItem(text = "Data Upload", tabName = "dataload"),
menuItem(text = "Box and Density Plots", tabName = "box"),
menuItem(text = "MeanSD Plot", tabName = "meansd"),
menuItem(text = "Mean vs Difference", tabName = "meandiff"),
conditionalPanel(
condition = "input.menu1 == 'meandiff'",
uiOutput("meandiff1")
),
menuItem(text = "Corrgram",tabName = "corrgram"),
menuItem(text = "Compare Replicates",tabName = "repvsrep"),
conditionalPanel(
condition = "input.menu1 == 'repvsrep'",
uiOutput("repvsrep1") ),
menuItem(text = "PCA", tabName = "pca"),
menuItem(text = "Heatmap", tabName = "testsigmoid"),
menuItem(text = "Linear Model", tabName = "volcano"),
conditionalPanel(
condition = "input.menu1 == 'volcano' & input.modtyp == 'lin'",
sliderInput(inputId = "pvalsli", label = "Change Pvalue threshold",min = 0,max = 0.1,value = 0.05),
sliderInput(inputId = "avthrssli", label = "Change avfold threshold",min = 0,max = 1,value = 0.2)
),
menuItem(text = "Sigmoidal fit",tabName = "sigfit"),
menuItem(text = "Summary", tabName = "summary"),
menuItem(text = "Download", tabName = "download"),
menuItem(text = "Session Log", tabName = "tst")
)
),
dashboardBody(
tabItems(
tabItem(tabName = 'tst',box(htmlOutput("sessionInfo"),width = 12)),
tabItem(tabName = "testsigmoid",
box(width = 12, height = 800,
plotOutput("plot9",height = 750)
)),
tabItem(tabName = "intro", includeHTML(path ="introduction.html")),
# The step by step has been removed from the app but can be re instated by including the menuItem at the start of the UI
tabItem(tabName = "stbyst",
conditionalPanel(condition = 'input.stage == "stage1"',
tabBox(id = 'stg1tabs', width = 12,
tabPanel(title = "Step 1",
h4("Go to the tab on the sidebar"),
br(),br()
,HTML('<p><img src="stage1step1.gif" height = 500 /></p>')
),
tabPanel(title = "Step 2",
h4("Select your data type, please note that intensities will take a few minutes to run."),
br(),HTML('<p><img src="stage1step2.gif" height = 450 /></p>')
),
tabPanel(title = "Step 3",
h4("Select the number of channels and replicates."),
br(),
HTML('<p><img src="stage1step3.gif" height = 450 /></p>')
),
tabPanel(title = "Step 4",
h4("Choose the columns from your data set which indicate the channels you would like to analyse. Note that you can search for these column names by typing in the input box."),
br(),h4("Remember to check that the uploaded column names correspond with the correct standardised name by looking at the table. You can change these positions by dragging and dropping the selected column names in the desired order in the input box."),
br(),HTML('<p><img src="stage1step4.gif" height = 450 /></p>')
),
tabPanel(title = "Step 5",
h4("(optional depending on input) If you would like to apply a sigmoidal fit and have an adequate amount of data, use the radio button to change the fit and input your concentrations, separating them with a comma
. Please Note that this may take a few minutes to run"),
br(),HTML('<p><img src="doschedasigmoid.gif" height = 450 /></p>')
),
tabPanel(title = "Step 6",
h4("(optional depending on input) If you are using intensities, you required to input the peptide quality score and sequence."),
br(),HTML('<p><img src="doschedaintensity.gif" height = 450 /></p>')),
tabPanel(title = "Step 7",
h4("Change to one of the plot tabs and you will see the loading sign appear in place of the logo, now cycle through all the tabs.")
)
)),
conditionalPanel(condition = 'input.stage == "stage2"'
,
tabBox(id = 'stg2tabs', width = 12,
tabPanel(title = "Stage 2",
h4(" Cycle through plots, this is done by clicking on the sidebar tabs and the tabs within the main panel.")
))
),
conditionalPanel(condition = 'input.stage == "stage3"'
,
tabBox(id = 'stg3tabs', width = 12,
tabPanel(title = "Download Data",
h4("Go to the Download tab and press the Download Data button to download the processed data in csv format. and use the ‘Download Report’ to download a html file with all your plots with descriptions with them to save your results from the pipeline.")
),
tabPanel(title = "Download Report",
h4("Go to the Download tab and press the ‘Download Report’ button to download a html file with all your plots with description, allowing you to save your results from the pipeline.")
)
)
)),
# End of the step by step
tabItem(tabName = "dataload",
box(width = 4,
fluidRow(column(5,radioButtons("datype", "Data Type:",
c("Intensities" = "intensity",
"Fold Change" = "FC",
"Log-Fold Change" = "lFC"))),
column(5,radioButtons("filetype", "File Type:",
c(".csv" = "CSV",
".txt" = "TXT",
".xlsx" = "XLSX")))
),
conditionalPanel(condition = 'input.datype == "intensity" & input.modtyp != "sigmoid"',
radioButtons("dorem", "Do removal:",
c("Yes" = "yes",
"No" = "no"),selected = 'no')
)
,
# DATA file upload
fileInput('file2', 'Choose file',
accept = c(".txt",".csv",".xlsx")),
fluidRow(column(5, numericInput("chans","# Channels",value = 4, min = 1)),
column(5, numericInput("reps","# Replicates",value = 1,min = 1))
),
actionButton("changenames", label = "Change Names"),
conditionalPanel(condition = "(input.changenames % 2) == 1",
uiOutput("setNames")
),
uiOutput("ui_choice"),
radioButtons(inputId = "normalize",label = 'Choose Normalization', choices =
c("LOESS" = "loess",
"Median" = "median",
"None" = "none"),
selected = 'loess'
),
conditionalPanel(condition = 'input.datype == "intensity"',
uiOutput("ui_sequence"),
uiOutput("ui_qual"),
numericInput('pearsvar',label = "Pearson Variable", value = 0.4,min = -1,max = 1,step = 0.1)
),
conditionalPanel(condition = 'input.toacc == true || input.datype == "intensity"',
uiOutput("ui_accession")
),
conditionalPanel(condition = 'input.toacc == true & input.datype != "intensity"',
uiOutput("ui_uniqpep")
),
conditionalPanel(condition = "input.modtyp == 'sigmoid'",
checkboxInput('incpd', 'Insert pulldown of pull down', value = FALSE)
),
conditionalPanel(condition = 'input.incpd == true',
uiOutput("ui_pdofpd")
),
conditionalPanel( condition = "input.datype != 'intensity'",
checkboxInput("toacc", "Data is NOT Proteome Discoverer 2.1", FALSE)
),
checkboxInput('genefile', 'Upload an Accession to Gene ID file', value = FALSE)
# uiOutput("ui_sequence"),
## remove column obselete
# fluidRow(
# column(5,conditionalPanel(
# condition = "input.conf != 0",
# actionButton(inputId = "removechan", label = "Remove Column")
# ))),
#
# conditionalPanel(
# condition = "(input.removechan % 2) == 1",
# uiOutput("remchan")
# )
),
box(width = 8,
DT::dataTableOutput("test")
),
box(width = 8,
conditionalPanel(condition = 'input.chans >= 5 & input.reps == 1',
radioButtons("modtyp", "Fit model:",
c("Sigmoidal" = "sigmoid",
"Linear" = "lin"
),selected = "lin")),
conditionalPanel(condition = 'input.chans < 5',
h1("Less than 5 channels, only a linear model can be applied")
),
conditionalPanel(condition = "input.modtyp == 'sigmoid'",
textInput("concsig", "Enter vector of concentrations from low to high [comma delimited]. Ensure these are not log concentrations"),
textOutput("concsig")
)
),
box(width = 8,
selectizeInput( 'organism',label = 'Select your organism:', choice = c('H.sapiens','C. familiaris','D.melanogaster','M. musculus','R. norvegicus', 'S.cerevisiae'), selected = 'H.sapiens'),
conditionalPanel(condition = 'input.genefile == true',
fluidRow(column(5,fileInput('geneF', 'Choose you Accession to Gene ID file',
accept = c(".txt",".csv",".xlsx"))),
column(5,radioButtons("generadio", "File Type:",
c(".csv" = "CSV",
".txt" = "TXT",
".xlsx" = "XLSX"))
))
)
)
),
tabItem(tabName = "box",
fluidRow(
tabBox(id = "tb1", width = 9, height = 700,
tabPanel("Box",plotOutput(height = 700, "bar")),
tabPanel("Density", plotOutput(height = 700, "plot2")),
tabPanel("Venn", plotOutput(height = 700, "venn"))
),
box(width = 3,
conditionalPanel(condition = "input.tb1 == 'Venn'",
checkboxInput(inputId = 'venninput' ,label = 'Include file', value = FALSE)
),
conditionalPanel('input.venninput == true',
radioButtons("filetype2", "File Type:",
c(".csv" = "CSV",
".txt" = "TXT",
".xlsx" = "XLSX")),
fileInput(inputId = 'venninp',label = 'Choose input file',
accept = c(".txt",".csv",".xlsx") )
)
)
)
),
tabItem(tabName = "meansd",
fluidRow(box(width = 9, height = 700, plotOutput(height = 600, "plot3")))),
tabItem(tabName = "meandiff",
fluidRow(
box(width = 9, height = 700, plotOutput(height = 600, "plot6"))
)),
tabItem("corrgram", fluidRow(box(width = 9, height = 800, plotOutput(height = 700,"plot5")))
),
tabItem("repvsrep", fluidRow(box(width = 9, height = 800, plotOutput(height = 700,"repvsrep")))),
tabItem(tabName = "pca", fluidRow( box(width = 9, height = 800, plotOutput(height = 700,"plot7")))),
tabItem(tabName = "volcano", fluidRow( tabBox(id = "volplots", width = 9, height = 800,
tabPanel(title = "P-Value Distribution",plotOutput(height = 700,"plot4")),
tabPanel(title = "Slope", plotOutput(height = 700,"plot8")),
tabPanel(title = "Intercept", plotOutput(height = 700,"volcanoint")),
tabPanel(title = "Quadratic", plotOutput(height = 700,"volcanoquad"))
))),
tabItem(tabName = "sigfit", fluidRow( tabBox(id = "sigplots", width = 10, height = 800,
tabPanel(title = "Difference Top-Bottom",plotOutput(height = 700,"DiffTopBottom")),
tabPanel(title = "RB50", plotOutput(height = 700,"RB50")),
tabPanel(title = "Slope", plotOutput(height = 700,"Slope_pl"))
))),
tabItem(tabName = "summary", fluidRow(
tabBox(id = "sumtab", width = 8,
tabPanel("Data p-values",div(DT::dataTableOutput("testmerge",width = '100%'),style = "font-size:90%")),
tabPanel("Kinases", DT::dataTableOutput("kintab"))
),box(title = "Corrgram QC", width = 4,
infoBoxOutput(outputId = "corrinfo",width = 12)
),box(title = "P Value QC", width = 4,
conditionalPanel(condition = "input.modtyp == 'sigmoid'",
infoBoxOutput("siginfodt",width = 12),
infoBoxOutput("siginfoslop",width = 12),
infoBoxOutput("siginfodiff",width = 12)
),
conditionalPanel(condition = "input.modtyp != 'sigmoid'",
infoBoxOutput(outputId = "infopvalslo",width = 12),
br(),br(),br(), br(),br(), br(),
infoBoxOutput(outputId = "infopvalint",width = 12),
br(),br(),br(), br(),br(), br(),
infoBoxOutput(outputId = "infopvalquad",width = 12)
)
)
)),
tabItem(tabName = "download",
box(width = 12,
textInput("dataset", "Filename for Data", value = "Doscheda"),
downloadButton('downloadData', 'Download Data'),
downloadButton("report", "Generate report")
),
box(width = 12,
conditionalPanel(condition = "input.datype == 'intensity'",
actionButton(inputId = 'intcalc',"Calculate Removed Peptides")
), br(),
conditionalPanel(condition = "input.intcalc != 0",
downloadButton('peprmv', "Download Removed Peptides")
)
)
)
)
)
))
#########################################################
## SERVER
#########################################################
server <- shinyServer(function(input, output) {
options(shiny.maxRequestSize=100*1024^2)
##############################################
## uniprot gene load in any changes to uni prot file will affect this section
uniprotGene <- reactive({
if(input$organism == 'H.sapiens'){
query = '<query model="genomic" view="Protein.primaryAccession Protein.uniprotAccession Protein.genes.symbol" sortOrder="Protein.primaryAccession ASC" >
<constraint path="Protein.organism.shortName" op="=" value="H. sapiens" code="A" />
</query>'
ret=POST('http://www.humanmine.org/humanmine/service/query/results',
body=list(query=query, format='json'),
encode='form')
} else if(input$organism == 'D. melanogaster'){
query = '<query model="genomic" view="Protein.primaryAccession Protein.uniprotAccession Protein.genes.symbol" sortOrder="Protein.primaryAccession ASC" >
<constraint path="Protein.organism.shortName" op="=" value="D. melanogaster" code="A" />
</query>'
ret=POST('http://www.flymine.org/flymine/service/query/results',
body=list(query=query, format='json'),
encode='form')
}else if(input$organism == 'M. musculus'){
query = '<query model="genomic" view="Protein.primaryAccession Protein.uniprotAccession Protein.genes.symbol" sortOrder="Protein.primaryAccession ASC" >
<constraint path="Protein.organism.shortName" op="=" value="M. musculus" code="A" />
</query>'
ret = POST('http://www.mousemine.org/mousemine/service/query/results',
body=list(query=query, format='json'),
encode='form')
}else if (input$organism == 'R. norvegicus'){
query = '<query model="genomic" view="Protein.primaryAccession Protein.uniprotAccession Protein.genes.symbol" sortOrder="Protein.primaryAccession ASC" >
<constraint path="Protein.organism.shortName" op="=" value="R. norvegicus" code="A" />
</query>'
ret = POST('http://www.ratmine.org/ratmine/service/query/results',
body=list(query=query, format='json'),
encode='form')
}else{
query = '<query model="genomic" view="Protein.primaryAccession Protein.uniprotAccession Protein.genes.symbol" sortOrder="Protein.primaryAccession ASC" >
<constraint path="Protein.organism.shortName" op="=" value="C. elegans" code="A" />
</query>'
ret=POST('http://www.humanmine.org/humanmine/service/query/results',
body=list(query=query, format='json'),
encode='form')
}
response = jsonlite::fromJSON(httr::content(ret,as='text'))
data.prots <- response$results[,c(1,3)]
colnames(data.prots) <- c('Entry','Gene.names')
as.data.frame(data.prots[,1:2],stringsAsFactors = FALSE)
})
## upload gene file
uploadGene <- reactive({
inFile <- input$geneF
if(is.null(inFile)){
return(NULL)
}
if( input$generadio == "TXT"){
file.rename(inFile$datapath,
paste(inFile$datapath, ".txt", sep=""))
# read.xlsx(paste(inFile$datapath, ".xlsx", sep=""),
# sheetIndex = 1, header = TRUE, stringsAsFactors = FALSE)
conv<- read.delim(paste(inFile$datapath, ".txt", sep=""),
header = TRUE,stringsAsFactors = FALSE)
} else if (input$generadio == "XLSX"){
file.rename(inFile$datapath,
paste(inFile$datapath, ".xlsx", sep=""))
# paste(inFile$datapath, ".xlsx", sep=""))
# read.xlsx(paste(inFile$datapath, ".xlsx", sep=""),
# sheetIndex = 1, header = TRUE, stringsAsFactors = FALSE)
conv<- read_excel(paste(inFile$datapath, ".xlsx", sep=""),
sheet = 1)
} else {
file.rename(inFile$datapath,
paste(inFile$datapath, ".csv", sep=""))
# paste(inFile$datapath, ".xlsx", sep=""))
# read.xlsx(paste(inFile$datapath, ".xlsx", sep=""),
# sheetIndex = 1, header = TRUE, stringsAsFactors = FALSE)
conv<- read.csv(paste(inFile$datapath, ".csv", sep=""), header = TRUE, stringsAsFactors = FALSE)
conv<- conv[,-1]
}
conv <- conv[,1:2]
colnames(conv) <- c('Entry', 'Gene.names')
conv
})
## venn diagram intersect file upload
uploadVenn <- reactive({
if(input$venninput == FALSE){
return(NULL)
} else{
inFile <- input$venninp
if(is.null(inFile)){
return(NULL)
}
if( input$filetype2 == "TXT"){
file.rename(inFile$datapath,
paste(inFile$datapath, ".txt", sep=""))
# read.xlsx(paste(inFile$datapath, ".xlsx", sep=""),
# sheetIndex = 1, header = TRUE, stringsAsFactors = FALSE)
conv<- read.delim(paste(inFile$datapath, ".txt", sep=""),
header = TRUE,stringsAsFactors = FALSE)
} else if (input$filetype2 == "XLSX"){
file.rename(inFile$datapath,
paste(inFile$datapath, ".xlsx", sep=""))
# paste(inFile$datapath, ".xlsx", sep=""))
# read.xlsx(paste(inFile$datapath, ".xlsx", sep=""),
# sheetIndex = 1, header = TRUE, stringsAsFactors = FALSE)
conv<- read_excel(paste(inFile$datapath, ".xlsx", sep=""),
sheet = 1)
} else {
file.rename(inFile$datapath,
paste(inFile$datapath, ".csv", sep=""))
# paste(inFile$datapath, ".xlsx", sep=""))
# read.xlsx(paste(inFile$datapath, ".xlsx", sep=""),
# sheetIndex = 1, header = TRUE, stringsAsFactors = FALSE)
conv<- read.csv(paste(inFile$datapath, ".csv", sep=""), header = TRUE, stringsAsFactors = FALSE)
conv<- conv[,-1]
}
conv
}
})
### crapome file upload
crapome<- reactive({
if(input$organism == 'S.cerevisiae'){
a <- read.csv('CRAPOME_YEAST',stringsAsFactors = FALSE)
} else{
a <- read.csv('CRAPOME_HUMAN',stringsAsFactors = FALSE)
}
print(head(a))
a
})
### DATA file upload
data <- reactive({
inFile <- input$file2
if(is.null(inFile)){
return(NULL)
}
if( input$filetype == "TXT"){
file.rename(inFile$datapath,
paste(inFile$datapath, ".txt", sep=""))
# read.xlsx(paste(inFile$datapath, ".xlsx", sep=""),
# sheetIndex = 1, header = TRUE, stringsAsFactors = FALSE)
conv<- read.delim(paste(inFile$datapath, ".txt", sep=""),
header = TRUE,stringsAsFactors = FALSE)
} else if (input$filetype == "XLSX"){
file.rename(inFile$datapath,
paste(inFile$datapath, ".xlsx", sep=""))
# paste(inFile$datapath, ".xlsx", sep=""))
# read.xlsx(paste(inFile$datapath, ".xlsx", sep=""),
# sheetIndex = 1, header = TRUE, stringsAsFactors = FALSE)
conv<- read_excel(paste(inFile$datapath, ".xlsx", sep=""),
sheet = 1)
} else {
file.rename(inFile$datapath,
paste(inFile$datapath, ".csv", sep=""))
# paste(inFile$datapath, ".xlsx", sep=""))
# read.xlsx(paste(inFile$datapath, ".xlsx", sep=""),
# sheetIndex = 1, header = TRUE, stringsAsFactors = FALSE)
conv<- read.csv(paste(inFile$datapath, ".csv", sep=""), header = TRUE, stringsAsFactors = FALSE)
}
data.frame(conv)
})
## ui elements
output$ui_accession<- renderUI({
temp <- data()
## using selectizeInput with drag_drop and DT
selectizeInput("accession", "Choose Accession", choices = colnames(temp) ,
selected = NULL,
multiple = FALSE,
options = list(plugins = list('remove_button')))
})
output$ui_uniqpep<- renderUI({
temp <- data()
## using selectizeInput with drag_drop and DT
selectizeInput("unipeps", "Choose Unique Peptides", choices = colnames(temp) ,
selected = NULL,
multiple = FALSE,
options = list(plugins = list('remove_button')))
})
output$ui_pdofpd<- renderUI({
temp <- data()
## using selectizeInput with drag_drop and DT
selectizeInput("pdofpd", "Choose Pulldown of pulldown", choices = colnames(temp) ,
selected = NULL,
multiple = FALSE,
options = list(plugins = list('remove_button')))
})
output$ui_sequence<- renderUI({
temp <- data()
## using selectizeInput with drag_drop and DT
selectizeInput("sequence", "Choose Sequence", choices = colnames(temp) ,
selected = NULL,
multiple = FALSE,
options = list(plugins = list('remove_button')))
})
output$ui_choice<- renderUI({
reqtemp <- data()
req(reqtemp)
## using selectizeInput with drag_drop and DT
selectizeInput("view_vars", "Select variables to show:", choices = colNamTot(),
selected = colNamSel(),
multiple = TRUE,
options = list(plugins = list('remove_button', 'drag_drop'), maxItems = nchans()))
})
output$ui_qual<- renderUI({
reqtemp <- data()
req(reqtemp)
## using selectizeInput with drag_drop and DT
selectizeInput("quality", "Select Peptide Qvality Score:", choices = colNamTot(),
selected = colNamSel(),
multiple = FALSE,
options = list(plugins = list('remove_button', 'drag_drop'), maxItems = 1))
})
output$remchan<- renderUI({
reqtemp <- data()
req(reqtemp)
selectizeInput(
'remchan', 'Choose Channels to remove', choices = finalNames(), multiple = TRUE,
options = list(plugins = list('remove_button'))
)
})
## final names setting
standardNames <- reactive({
if(input$datype == "intensity"){
out<- paste("rep",rep(1:input$reps,each = input$chans),"_",
rep(paste("C",c("ontrol",0:(input$chans - 2)), sep = ""),input$reps),sep = "")
vals$labelNames = setNames(out, out)
}else{
out<- paste("rep",rep(1:input$reps,each = input$chans),"_",
rep(paste("C",0:(input$chans - 1), sep = ""),input$reps),sep = "")
vals$labelNames = setNames(out, out)
}
return(out)
})
output$setNames <- renderUI({
list(
h4("Change Names")
, selectInput("nameToChange", "Standard name"
, names(vals$labelNames))
, textInput("labelToAdd", "Change to")
, actionButton("makeLabel", "Set label")
)
})
observeEvent(input$makeLabel, {
vals$labelNames[input$nameToChange] <- input$labelToAdd
})
finalNames<- reactive({
vals$labelNames
})
##############################################
sigConc <- reactive({
if(input$modtyp == "sigmoid"){
sort(as.numeric(unlist(strsplit(input$concsig,","))))
}else{
return(NULL)
}
})
output$concsig <- renderText({
x <- as.numeric(unlist(strsplit(input$concsig,",")))
if(input$datype== 'intensity'){
n<- input$chans - 1
}else{
n <- input$chans*input$reps
}
if(length(x) < n){
paste0("Not enough concentrations, please put ",n," concentrations")
} else if(length(x) > n){
paste0("Too many concentrations, please put ",n," concentrations")
}else{
x<- sort(x)
print(c("Concentrations:",x))
}
})
output$selectnames <- renderUI({
selectizeInput("selectnames", "Change Names", choices = standardNames(),
options = list(maxOptions = input$reps * input$chans))
})
vals <- reactiveValues(
labelNames = character()
)
#### LABEL UPLOAD
#### data imported and finalNames is vector of colnames ####
rReps <- reactive({
input$reps
})
nchans <- reactive({
input$reps * input$chans
})
### probably dont need this
### datachange table
### selectize
colNamTot<- reactive({
reqtemp <- data()
req(reqtemp)
a2 <- data()
colnames(a2)
})
colNamSel<- reactive({
a1 <- data()
a1 <- colnames(a1)
sample(a1,nchans())
})
indexmatrix <- reactive({
reqtemp <- data()
req(reqtemp)
if(input$reps <= 1){
NULL
} else {
if(input$datype == "intensity"){
channe <- channels()
reps <- input$reps
chans <- input$chans - 1
ser <- finalNames()
ser<- ser[-seq(1,by = input$chans,length.out = input$reps)]
}else{
ser <- finalNames()
channe <- channels()
reps <- input$reps
chans <- input$chans
}
combinations <- t(combn(reps,2))
combmat<- matrix(rep(as.vector(t(combinations)),chans),ncol = 2,byrow = TRUE)
# create factor for repeat ...
name.vec <- 1:(chans*reps)
repfac <- rep(1:chans,times = reps)
index <- rep(0:(reps-1),each = chans)
combfac<- rep(1:(reps),each = chans)
# total combinations = chans * nrow()
columnindex <- matrix(0 , ncol = 5 , nrow = chans * nrow(combinations) )
colnames(columnindex) <- c("concentration","rep1","rep2","index1","index2")
columnindex[,1] <- rep(1:chans ,each = nrow(combinations))
columnindex[,2:3]<- combmat
columnindex
# create matrix which will be indexed by first 3 columns of column index
index.mat <- matrix(name.vec,ncol = reps)
for(i in 1:nrow(columnindex)){
columnindex[i,4] <- index.mat[columnindex[i,1],columnindex[i,2]]
columnindex[i,5] <- index.mat[columnindex[i,1],columnindex[i,3]]
}
dadt <- dataMerge()
create.names <- rep("", nrow(columnindex))
for( i in 1:nrow(columnindex)){
create.names[i] <- paste(ser[columnindex[i,4]], "vs", ser[columnindex[i,5]])
}
final.mat <- data.frame(names = create.names,columnindex)
final.mat
final.mat[!is.na(rowSums(matrix(match(columnindex,channe),ncol=5))),]
}
})
selRemCol <- reactive({
reqtemp <- data()
req(reqtemp)
a1<- finalNames()
a1<- as.character(a1)
if(is.null(input$remchan)){
0
}else{
-match(input$remchan,a1)
}
})
channels <- reactive({
reqtemp <- data()
req(reqtemp)
if(input$datype == 'intensity'){
if(input$reps == 1){
1:(input$chans*input$reps -1)
}else{
1:(input$chans*input$reps -2)
}
}else{
a1 <- selRemCol()
vec <- 1:nchans()
if(a1 != 0){
vec <- vec[selRemCol()]
}
vec
}
})
##### DATA HANDLING #####
## Intensities
intData <- reactive({
if(input$datype == "intensity"){
tempdat <- data()
# make matrix of descriptions and accessions to filter by common proteins
accDesMat<- as.character(tempdat[as.character(tempdat[,input$accession]) == "",c(input$accession)])
if(input$incpd == TRUE){
data.merged <- tempdat[,c(input$view_vars, input$accession, input$sequence,input$quality,input$pdofpd)]
}else{
data.merged <- tempdat[,c(input$view_vars, input$accession, input$sequence,input$quality)]
}
channelnames <- standardNames()
repindex <- rep(1:input$reps,each = input$chans)
totfal <- rep(FALSE , (input$chans + 3 ))
if(input$incpd == TRUE){
newdf <- cbind(data.merged[,1:input$chans], data.merged[,c(input$accession, input$sequence,input$quality,input$pdofpd)])
colnames(newdf) <- c(channelnames[repindex == 1],"Accession","Sequence", "Quality",'Kd')
newdf <- newdf[!is.na(rowSums(newdf[,1:input$chans])),]
newdf <- newdf[newdf$Quality <= 0.05, ]
newdf <- data.frame(newdf, outliers = rep(0,length(newdf[,1])), uniquePeps = rep(0,length(newdf[,1])), addedVals = rep(0,length(newdf[,1])),Kd = newdf$Kd)
}else{
newdf <- cbind(data.merged[,1:input$chans], data.merged[,c(input$accession, input$sequence,input$quality)])
colnames(newdf) <- c(channelnames[repindex == 1],"Accession","Sequence", "Quality")
newdf <- newdf[!is.na(rowSums(newdf[,1:input$chans])),]
newdf <- newdf[newdf$Quality <= 0.05, ]
}
if(input$reps == 2){
channelnames <- paste("rep",rep(1:input$reps,each = input$chans),"_",
rep(paste("C",c("ontrol",0:(input$chans - 2)), sep = ""),input$reps),sep = "")
newdf2 <- cbind(data.merged[,(input$chans+1):(2*input$chans) ],data.merged[,c(input$accession, input$sequence,input$quality)])
colnames(newdf2) <- c(channelnames[repindex == 2],"Accession","Sequence","Quality")
newdf2 <- newdf2[!is.na(rowSums(newdf2[,1:input$chans])),]
newdf2 <- newdf2[newdf2$Quality <= 0.05, ]
newdf <- data.frame(newdf, outliers = rep(0,length(newdf[,1])), uniquePeps = rep(0,length(newdf[,1])), addedVals = rep(0,length(newdf[,1])))
newdf2 <- data.frame(newdf2, outliers = rep(0,length(newdf2[,1])), uniquePeps = rep(0,length(newdf2[,1])), addedVals = rep(0,length(newdf2[,1])))
common.proteins <- intersect(unique(newdf$Accession),unique(newdf2$Accession))
newdf <- newdf[!is.na(match(newdf$Accession,common.proteins)),]
newdf2 <- newdf2[!is.na(match(newdf2$Accession,common.proteins)),]
}else{
common.proteins <- unique(newdf$Accession)
}
if(input$dorem == "no"){
if(input$reps == 1){
if(input$incpd == TRUE){
prot1 <- unique(newdf$Accession)
sumkd <- rep(0,length(prot1))
protdf<- newdf[1:length(prot1),colnames(newdf) != "Sequence"]
for(i in 1:length(prot1)){
## grep for total intensity () includes non unique peps
protdf[i,1:input$chans] <- apply(newdf[grep(prot1[i],newdf$Accession),1:input$chans],2,sum,na.rm = TRUE)
protdf$Kd[i] <- sum(newdf$Kd[grep(prot1[i],newdf$Accession)],na.rm = TRUE)
protdf$Accession[i] <- prot1[i]
## use == to get unique peptides per protein per repeat
# protdf$uniquePeps[i] <- length(unique(newdf$Sequence[newdf$Accession == prot1[i]]))
protdf$uniquePeps[i] <- length(unique(unique(newdf$Sequence[newdf$Accession == prot1[i]])))
}
protdf$uniquePeps[grep(";",protdf$Accession)] <- 0
fc1 <- protdf[,1] / protdf[,2:input$chans]
Kd <- protdf$Kd / protdf[,1]
fcprotdf <- data.frame(log2(fc1),
Accession = protdf$Accession,uniquePepr1 = protdf$uniquePeps,
uniquePepr2 =protdf$uniquePeps, Kd = Kd)
fcprotdf<- fcprotdf[!is.na(rowSums(fcprotdf[1:(input$chans - 1 )])),]
fcprotdf
}else{
prot1 <- unique(newdf$Accession)
protdf<- newdf[1:length(prot1),colnames(newdf) != "Sequence"]
for(i in 1:length(prot1)){
## grep for total intensity () includes non unique peps
protdf[i,1:input$chans] <- apply(newdf[grep(prot1[i],newdf$Accession),1:input$chans],2,sum,na.rm = TRUE)
protdf$Accession[i] <- prot1[i]
## use == to get unique peptides per protein per repeat
# protdf$uniquePeps[i] <- length(unique(newdf$Sequence[newdf$Accession == prot1[i]]))
protdf$uniquePeps[i] <- length(unique(unique(newdf$Sequence[newdf$Accession == prot1[i]])))
}
protdf$uniquePeps[grep(";",protdf$Accession)] <- 0
fc1 <- protdf[,1] / protdf[,2:input$chans]
fcprotdf <- data.frame(log2(fc1),
Accession = protdf$Accession,uniquePepr1 = protdf$uniquePeps,
uniquePepr2 =protdf$uniquePeps)
fcprotdf<- fcprotdf[!is.na(rowSums(fcprotdf[1:(input$chans - 1 )])),]
fcprotdf
}
}else{
prot1 <- unique(newdf$Accession)
protdf<- newdf[1:length(prot1),colnames(newdf) != "Sequence"]
for(i in 1:length(prot1)){
## grep for total intensity () includes non unique peps
protdf[i,1:input$chans] <- apply(newdf[grep(prot1[i],newdf$Accession),1:input$chans],2,sum,na.rm = TRUE)
protdf$Accession[i] <- prot1[i]
## use == to get unique peptides per protein per repeat
# protdf$uniquePeps[i] <- length(unique(newdf$Sequence[newdf$Accession == prot1[i]]))
protdf$uniquePeps[i] <- length(unique(c(unique(newdf$Sequence[newdf$Accession == prot1[i]]),unique(newdf2$Sequence[newdf2$Accession == prot1[i]]))))
}
protdf$uniquePeps[grep(";",protdf$Accession)] <- 0
prot2 <- unique(newdf2$Accession)
### second data frame
protdf2<- newdf2[1:length(prot2),colnames(newdf2) != "Sequence"]
for(i in 1:length(prot2)){
## grep for total intensity () includes non unique peps
protdf2[i,1:input$chans] <- apply(newdf2[grep(prot2[i],newdf2$Accession),1:input$chans],2,median,na.rm = TRUE)
protdf2$Accession[i] <- prot2[i]
## use == to get unique peptides per protein per repeat
protdf2$uniquePeps[i] <- length(unique(newdf2$Sequence[newdf2$Accession == prot2[i]]))
}
protdf2$uniquePeps[grep(";",protdf2$Accession)] <- 0
com.prot <- intersect(protdf$Accession,protdf2$Accession)
fc1 <- protdf[,1] / protdf[,2:input$chans]
fc2 <- protdf2[,1] / protdf2[,2:input$chans]
fcprotdf <- data.frame(log2(fc1[match(com.prot,protdf$Accession),]),
log2(fc2[match(com.prot,protdf2$Accession),]),
Accession = com.prot,uniquePepr1 = protdf$uniquePeps[match(com.prot,protdf$Accession)],
uniquePepr2 =protdf2$uniquePeps[match(com.prot,protdf2$Accession)])
fcprotdf<- fcprotdf[!is.na(rowSums(fcprotdf[1:(input$reps*input$chans -2 )])),]
fcprotdf
}
}else{
totpepdf <- NULL
totpepdf2 <- NULL
for (z in 1:length(common.proteins)){
temp <- newdf[newdf$Accession == common.proteins[z],]
temp2 <- newdf2[newdf2$Accession == common.proteins[z],]
# first step: check if all peptides are unique ...
if(all.equal(grep(";",temp$Accession),integer(0)) == TRUE){
uniPeptides1 <- length(unique(temp$Sequence))
} else {
uniPeptides1 <- length(unique(temp$Sequence[-grep(";",temp$Accession)]))
}
if(all.equal(grep(";",temp2$Accession),integer(0)) == TRUE){
uniPeptides2 <- length(unique(temp2$Sequence))
}else{
uniPeptides2 <- length(unique(temp2[-grep(";",temp2$Accession)]))
}
## add unique peptide column
temp$uniquePeps <- uniPeptides1
temp2$uniquePeps <- uniPeptides2
tempPep <- intersect(unique(temp$Sequence),unique(temp2$Sequence))
if(all.equal(tempPep, character(0)) == TRUE){
next
}
for(i in 1:length(tempPep)){
if(sum(temp$Sequence == tempPep[i]) != sum(temp2$Sequence == tempPep[i])){
dr <- peptide.match(temp[temp$Sequence == tempPep[i],],temp2[temp2$Sequence == tempPep[i],],input$chans)
dr1 <- dr$dr1
dr2 <- dr$dr2
} else {
dr1 <- temp[temp$Sequence == tempPep[i],]
dr2 <- temp2[temp2$Sequence == tempPep[i],]
}
tempoindex <- rep(FALSE,nrow(dr1))
for(j in 1:nrow(dr1)){
percor <- cor.test(log2(as.numeric(dr1[j,1:input$chans])),log2(as.numeric(dr2[j,1:input$chans])))
tempoindex[j] <- percor$estimate < input$pearsvar
}
dr1[tempoindex,1:input$chans] <- NA
dr2[tempoindex,1:input$chans] <- NA
tempReplace <- dr1
tempReplace2 <- dr2
temp <- temp[temp$Sequence != tempPep[i],]
temp <- rbind(temp,tempReplace)
temp2 <- temp2[temp2$Sequence != tempPep[i],]
temp2 <- rbind(temp2,tempReplace2)
}
temp<- temp[match(tempPep,temp$Sequence),]
temp2<- temp2[match(tempPep,temp2$Sequence),]
# newdf <- newdf[newdf$Accession != common.proteins[z],]
# newdf<- rbind(newdf,temp)
totpepdf <- rbind(totpepdf,temp)
# newdf2 <- newdf2[newdf2$Accession != common.proteins[z],]
# newdf2<- rbind(newdf2,temp2)
totpepdf2 <- rbind(totpepdf2,temp2)
}
totpepdf<- totpepdf[!is.na(rowSums(totpepdf[,1:input$chans])),]
totpepdf2<- totpepdf2[!is.na(rowSums(totpepdf2[,1:input$chans])),]
totpepdf<- totpepdf[totpepdf$addedVals == 0, ]
totpepdf<- totpepdf[totpepdf$addedVals == 0, ]
totpepdf$uniquePeps[grep(';',totpepdf$Accession)] <- 0
### take sums
pepframe<- data.frame(totpepdf[1:length(common.proteins),1:input$chans],totpepdf2[1:length(common.proteins),1:input$chans],
Accession = totpepdf$Accession[1:length(common.proteins)], uniquePeps = totpepdf$uniquePeps[1:length(common.proteins)])
pepsum1 <- pepsum2 <- totpepdf[1:length(common.proteins),]
pepsum1 <- pepsum1[,-match(c("Sequence","addedVals", "Quality","outliers"),colnames(pepsum1))]
pepsum2 <- pepsum2[,-match(c("Sequence","addedVals", "Quality","outliers"),colnames(pepsum2))]
pepsum1$pepNum <- pepsum1$pepNum <- rep(0,length(common.proteins))
colnames(pepsum2)[1:input$chans]<- channelnames[(input$chans+1):(input$chans*input$reps)]
for(i in 1:length(common.proteins)){
pepsum1[i,1:input$chans] <- colSums(totpepdf[grep(common.proteins[i],totpepdf$Accession),1:input$chans])
pepsum2[i,1:input$chans] <- colSums(totpepdf2[grep(common.proteins[i],totpepdf2$Accession),1:input$chans])
pepsum1$pepNum[i] <- nrow(totpepdf[grep(common.proteins[i],totpepdf$Accession),1:input$chans])
pepsum2$pepNum[i] <- nrow(totpepdf2[grep(common.proteins[i],totpepdf2$Accession),1:input$chans])
pepsum1$Accession[i]<- pepsum2$Accession[i] <- common.proteins[i]
pepsum1$uniquePeps[i]<- totpepdf$uniquePeps[as.logical(match(totpepdf$Accession,common.proteins[i],nomatch = FALSE))][1]
# pepframe[i, 1:input$chans] <- apply( totpepdf[totpepdf$Accession == common.proteins[i], 1:input$chans],2, sum)
# pepframe[i, (input$chans+1):(input$chans*input$reps)] <- apply( totpepdf2[totpepdf2$Accession == common.proteins[i], 1:input$chans],2, sum)
#
# pepframe$Accession <- common.proteins[i]
# pepframe$uniquePeps <- totpepdf$uniquePeps[totpepdf$Accession == common.proteins[i]][1]
}
indexpepsum <- ((rowSums(pepsum1[1:input$chans]) != 0) + ((rowSums(pepsum2[1:input$chans])) != 0)) == 2
pepsum1<- pepsum1[indexpepsum, ]
pepsum2<- pepsum2[indexpepsum, ]
# indpepsum2 <- pepsum1$pepNum > 1 | pepsum2$pepNum > 1
# pepsum1 <- pepsum1[indpepsum2,]
# pepsum2 <- pepsum1[indpepsum2,]
fc1 <- pepsum1[,1] / pepsum1[,2:input$chans]
fc2 <- pepsum2[,1] / pepsum2[,2:input$chans]
fcprotdf <- data.frame(log2(fc1),log2(fc2),pepsum1$Accession,uniquePepr1 = pepsum1$uniquePeps,
uniquePepr2 = pepsum2$uniquePeps,num1 = pepsum1$pepNum, num2 = pepsum2$pepNum )
fcprotdf
}
fcprotdf
}else{
return(NULL)
}
})
######################################################### isolate removed peptides
pepdwn <- reactive({
if(input$intcalc == 0){
return(NULL)
}else{
tempdat <- data()
# make matrix of descriptions and accessions to filter by common proteins
accDesMat<- as.character(tempdat[as.character(tempdat[,input$accession]) == "",c(input$accession)])
data.merged <- tempdat[,c(input$view_vars, input$accession, input$sequence,input$quality)]
channelnames <- standardNames()
repindex <- rep(1:input$reps,each = input$chans)
totfal <- rep(FALSE , (input$chans + 3 ))
newdf <- cbind(data.merged[,1:input$chans], data.merged[,c(input$accession, input$sequence,input$quality)])
colnames(newdf) <- c(channelnames[repindex == 1],"Accession","Sequence", "Quality")
newdf <- newdf[!is.na(rowSums(newdf[,1:input$chans])),]
newdf <- newdf[newdf$Quality <= 0.05, ]
newdf2 <- cbind(data.merged[,(input$chans+1):(2*input$chans) ],data.merged[,c(input$accession, input$sequence,input$quality)])
colnames(newdf2) <- c(channelnames[repindex == 2],"Accession","Sequence","Quality")
newdf2 <- newdf2[!is.na(rowSums(newdf2[,1:input$chans])),]
newdf2 <- newdf2[newdf2$Quality <= 0.05, ]
newdf <- data.frame(newdf, outliers = rep(0,length(newdf[,1])), uniquePeps = rep(0,length(newdf[,1])), addedVals = rep(0,length(newdf[,1])))
newdf2 <- data.frame(newdf2, outliers = rep(0,length(newdf2[,1])), uniquePeps = rep(0,length(newdf2[,1])), addedVals = rep(0,length(newdf2[,1])))
common.proteins <- intersect(unique(newdf$Accession),unique(newdf2$Accession))
newdf <- newdf[!is.na(match(newdf$Accession,common.proteins)),]
newdf2 <- newdf2[!is.na(match(newdf2$Accession,common.proteins)),]
totpepdf <- NULL
totpepdf2 <- NULL
for (z in 1:length(common.proteins)){
temp <- newdf[newdf$Accession == common.proteins[z],]
temp2 <- newdf2[newdf2$Accession == common.proteins[z],]
# first step: check if all peptides are unique ...
if(all.equal(grep(";",temp$Accession),integer(0)) == TRUE){
uniPeptides1 <- length(unique(temp$Sequence))
} else {
uniPeptides1 <- length(unique(temp$Sequence[-grep(";",temp$Accession)]))
}
if(all.equal(grep(";",temp2$Accession),integer(0)) == TRUE){
uniPeptides2 <- length(unique(temp2$Sequence))
}else{
uniPeptides2 <- length(unique(temp2[-grep(";",temp2$Accession)]))
}
## add unique peptide column
temp$uniquePeps <- uniPeptides1
temp2$uniquePeps <- uniPeptides2
tempPep <- intersect(unique(temp$Sequence),unique(temp2$Sequence))
if(all.equal(tempPep, character(0)) == TRUE){
next
}
for(i in 1:length(tempPep)){
if(sum(temp$Sequence == tempPep[i]) != sum(temp2$Sequence == tempPep[i])){
dr <- peptide.match(temp[temp$Sequence == tempPep[i],],temp2[temp2$Sequence == tempPep[i],],input$chans)
dr1 <- dr$dr1
dr2 <- dr$dr2
} else {
dr1 <- temp[temp$Sequence == tempPep[i],]
dr2 <- temp2[temp2$Sequence == tempPep[i],]
}
tempoindex <- rep(FALSE,nrow(dr1))
for(j in 1:nrow(dr1)){
percor <- cor.test(log2(as.numeric(dr1[j,1:input$chans])),log2(as.numeric(dr2[j,1:input$chans])))
tempoindex[j] <- percor$estimate < input$pearsvar
}
dr1[tempoindex,1:input$chans] <- NA
dr2[tempoindex,1:input$chans] <- NA
tempReplace <- dr1
tempReplace2 <- dr2
temp <- temp[temp$Sequence != tempPep[i],]
temp <- rbind(temp,tempReplace)
temp2 <- temp2[temp2$Sequence != tempPep[i],]
temp2 <- rbind(temp2,tempReplace2)
}
temp<- temp[match(tempPep,temp$Sequence),]
temp2<- temp2[match(tempPep,temp2$Sequence),]
# newdf <- newdf[newdf$Accession != common.proteins[z],]
# newdf<- rbind(newdf,temp)
totpepdf <- rbind(totpepdf,temp)
# newdf2 <- newdf2[newdf2$Accession != common.proteins[z],]
# newdf2<- rbind(newdf2,temp2)
totpepdf2 <- rbind(totpepdf2,temp2)
}
totpepdf<- totpepdf[!is.na(rowSums(totpepdf[,1:input$chans])),]
totpepdf2<- totpepdf2[!is.na(rowSums(totpepdf2[,1:input$chans])),]
totpepdf<- totpepdf[totpepdf$addedVals == 0, ]
totpepdf<- totpepdf[totpepdf$addedVals == 0, ]
totpepdf$uniquePeps[grep(';',totpepdf$Accession)] <- 0
### take sums
pepframe<- data.frame(totpepdf[1:length(common.proteins),1:input$chans],totpepdf2[1:length(common.proteins),1:input$chans],
Accession = totpepdf$Accession[1:length(common.proteins)], uniquePeps = totpepdf$uniquePeps[1:length(common.proteins)])
pepsum1 <- pepsum2 <- totpepdf[1:length(common.proteins),]
pepsum1 <- pepsum1[,-match(c("Sequence","addedVals", "Quality","outliers"),colnames(pepsum1))]
pepsum2 <- pepsum2[,-match(c("Sequence","addedVals", "Quality","outliers"),colnames(pepsum2))]
pepsum1$pepNum <- pepsum1$pepNum <- rep(0,length(common.proteins))
colnames(pepsum2)[1:input$chans]<- channelnames[(input$chans+1):(input$chans*input$reps)]
for(i in 1:length(common.proteins)){
pepsum1[i,1:input$chans] <- colSums(totpepdf[grep(common.proteins[i],totpepdf$Accession),1:input$chans])
pepsum2[i,1:input$chans] <- colSums(totpepdf2[grep(common.proteins[i],totpepdf2$Accession),1:input$chans])
pepsum1$pepNum[i] <- nrow(totpepdf[grep(common.proteins[i],totpepdf$Accession),1:input$chans])
pepsum2$pepNum[i] <- nrow(totpepdf2[grep(common.proteins[i],totpepdf2$Accession),1:input$chans])
pepsum1$Accession[i]<- pepsum2$Accession[i] <- common.proteins[i]
pepsum1$uniquePeps[i]<- totpepdf$uniquePeps[as.logical(match(totpepdf$Accession,common.proteins[i],nomatch = FALSE))][1]
}
indexpepsum <- ((rowSums(pepsum1[1:input$chans]) != 0) + ((rowSums(pepsum2[1:input$chans])) != 0)) == 2
pepsum1<- pepsum1[indexpepsum, ]
pepsum2<- pepsum2[indexpepsum, ]
end <- -row.match(newdf[,1:(input$chans+2)],totpepdf[,1:(input$chans+2)])
end2 <- -row.match(newdf2[,1:(input$chans+2)],totpepdf2[,1:(input$chans+2)])
rempep <- newdf[end,]
rempep2 <- newdf2[end2,]
colnames(rempep)<- paste("r1_",colnames(rempep),sep = '')
colnames(rempep2)<- paste("r2_",colnames(rempep2),sep = '')
if(nrow(rempep) > nrow(rempep2)){
finalrempep <- rempep
finalrempep[] <- NA
finalrempep[1:nrow(rempep2),]<- rempep2
finalrempep<- cbind(rempep,finalrempep)
}else{
finalrempep <- rempep2
finalrempep[] <- NA
finalrempep[1:nrow(rempep),] <- rempep
finalrempep <- cbind(finalrempep,rempep2)
}
colnames(finalrempep)<- c(paste("r1_",colnames(rempep),sep = ''),paste("r2_",colnames(rempep2),sep = ''))
finalrempep
}
})
## log fold changes
dataMerge <- reactive({
# testingkd <- rKd()
# print(head(testingkd))
inten <- intData()
if(input$datype != "intensity"){
if(input$modtyp == "sigmoid"){
data_orig2 <- data()
## if user has specified accession & Description
if(input$toacc == FALSE){
pattern<-"GN=(\\S+)"
g_fromD1<-str_extract(data_orig2$Description,pattern)
gID_D1a<-str_split_fixed(g_fromD1,"GN=",n=2)
gID_D1a<-as.vector(gID_D1a[,2])
gID_D1<-as.matrix(replace(gID_D1a,gID_D1a=="","NA"))
#Addition of the gene ID column
data_orig2["geneID"]<- (gID_D1)
}else{
if(input$genefile == FALSE){
tempacc <- data_orig2[,input$accession]
data_orig2 <- data_orig2[,(-input$accession)]
data_orig2$Accession <- tempacc
uniGene <- uniprotGene()
#uniGene$Gene.names <- gsub(' .*','',uniGene$Gene.names)
uniGene$Gene.names[uniGene$Gene.names == '']<- NA
GeneID <- uniGene$Gene.names[match(data_orig2$Accession,uniGene$Entry)]
GeneID <- make.names(GeneID,unique = TRUE)
data_orig2$geneID <- GeneID
}else{
tempacc <- data_orig2[,input$accession]
data_orig2 <- data_orig2[,(-input$accession)]
data_orig2$Accession <- tempacc
uniGene <- uploadGene()
GeneID <- uniGene$Gene.names[match(data_orig2$Accession,uniGene$Entry)]
GeneID <- make.names(GeneID,unique = TRUE)
data_orig2$geneID <- GeneID
data_orig2<-na.omit(data_orig2)
}
}
if(input$incpd == TRUE){
if(input$toacc == FALSE){
data.merged<-data.frame(data_orig2[,input$view_vars],
data_orig2$Accession, data_orig2$geneID,
data_orig2$X..Unique.Peptides,data_orig2[,input$pdofpd])
}else{
data.merged<-data.frame(data_orig2[,input$view_vars],
data_orig2$Accession, data_orig2$geneID,
data_orig2[,input$unipeps],data_orig2[,input$pdofpd])
}
final.Names <- finalNames()
colnames(data.merged)<- c(final.Names,
"Accession", "GeneID","UniquePeps",'Kd')
tmp<-data.merged[,1:input$chans]
tf <- as.data.frame(lapply(tmp, function(x) (is.na(x))))
countsNAs<-as.data.frame(apply(tf,1,function(x)table(x)["TRUE"]))
n_of_miss<-as.data.frame(as.numeric(str_replace_all(as.list(countsNAs[,1]),"NA",'0')))
data.merged <- data.frame(data.merged,n_of_miss)
colnames(data.merged)<-c( final.Names,
"Accession", "GeneID","UniquePeps",'Kd', "MissingVal")
#
missing_val <- 0
#
data.merged<- as.data.frame(data.merged[data.merged$MissingVal <= missing_val, ])
data.merged<-na.omit(data.merged)
#
# #Specify the number of missing points.For zero missing point is ==0
#
# #filiter for 2 unique peptides
data.merged <- data.merged[data.merged$UniquePeps > 1, ]
data.merged<-na.omit(data.merged)
#
#
if(input$normalize == 'loess' ){
data.merged <- data.frame(log2(normalize.loess(2^(data.merged[,channels()]))),
Accession=data.merged$Accession,
GeneID=data.merged$GeneID,
UniquePeps=data.merged$UniquePeps,
Kd = 1 / data.merged$Kd,
MissingVal=data.merged$MissingVal)
}else if(input$normalize == 'median'){
data.merged <- data.frame(log2( sweep( (2^(data.merged[,channels()]) ) ,
MARGIN = 2,
as.numeric(apply((2^(data.merged[,channels()])),2,median)),
FUN = "/")
),
Accession=data.merged$Accession,
GeneID=data.merged$GeneID,
UniquePeps=data.merged$UniquePeps,
Kd = 1 / data.merged$Kd,
MissingVal=data.merged$MissingVal)
}else{
data.merged <- data.frame(((2^(data.merged[,channels()]))),
Accession=data.merged$Accession,
GeneID=data.merged$GeneID,
UniquePeps=data.merged$UniquePeps,
Kd = 1 / data.merged$Kd,
MissingVal=data.merged$MissingVal)
}
data.merged<-na.omit(data.merged)
data.merged
} else {
if(input$toacc == FALSE){
data.merged<-data.frame(data_orig2[,input$view_vars],
data_orig2$Accession, data_orig2$geneID,
data_orig2$X..Unique.Peptides)
}else{
data.merged<-data.frame(data_orig2[,input$view_vars],
data_orig2$Accession, data_orig2$geneID,
data_orig2[,input$unipeps])
}
final.Names <- finalNames()
colnames(data.merged)<- c(final.Names,
"Accession", "GeneID","UniquePeps")
tmp<-data.merged[,1:input$chans]
tf <- as.data.frame(lapply(tmp, function(x) (is.na(x))))
countsNAs<-as.data.frame(apply(tf,1,function(x)table(x)["TRUE"]))
n_of_miss<-as.data.frame(as.numeric(str_replace_all(as.list(countsNAs[,1]),"NA",'0')))
data.merged <- data.frame(data.merged,n_of_miss)
colnames(data.merged)<-c( final.Names,
"Accession", "GeneID","UniquePeps","MissingVal")
#
missing_val <- 0
#
data.merged<- as.data.frame(data.merged[data.merged$MissingVal <= missing_val, ])
#
# #Specify the number of missing points.For zero missing point is ==0
#
# #filiter for 2 unique peptides
data.merged <- data.merged[data.merged$UniquePeps > 1, ]
#
#
if(input$normalize == 'loess'){
data.merged <- data.frame(log2(normalize.loess(2^(data.merged[,channels()]))),
Accession=data.merged$Accession,
GeneID=data.merged$GeneID,
UniquePeps=data.merged$UniquePeps,
MissingVal=data.merged$MissingVal)
}else if (input$normalize == 'median'){
data.merged <- data.frame(log2( sweep( (2^(data.merged[,channels()]) ) ,
MARGIN = 2,
as.numeric(apply((2^(data.merged[,channels()])),2,median)),
FUN = "/")
),
Accession=data.merged$Accession,
GeneID=data.merged$GeneID,
UniquePeps=data.merged$UniquePeps,
MissingVal=data.merged$MissingVal)
}else{
data.merged <- data.frame(log2(2^(data.merged[,channels()])),
Accession=data.merged$Accession,
GeneID=data.merged$GeneID,
UniquePeps=data.merged$UniquePeps,
MissingVal=data.merged$MissingVal)
}
data.merged<-na.omit(data.merged)
data.merged
}
} else {
tempdat <- data()
temp<- channels()
nvec <- length(temp)
data.merged <- tempdat[,input$view_vars]
colnames(data.merged) <- finalNames()
data.names<- c(input$view_vars,"Accession", "GeneID","UniquePeps","MissingVal")
if(input$datype == "FC"){
data.merged[,temp] <- log2(data.merged[,temp])
}
#tidy below !!
if(input$toacc == FALSE){
pattern<-"GN=(\\S+)"
g_fromD1<-str_extract(tempdat$Description,pattern)
gID_D1a<-str_split_fixed(g_fromD1,"GN=",n=2)
gID_D1a<-as.vector(gID_D1a[,2])
gID_D1<-as.matrix(replace(gID_D1a,gID_D1a=="","NA"))
Accession <- tempdat$Accession
UniquePeps <- MissingVal<- tempdat[,grep("Unique",colnames(tempdat))]
data.merged <- cbind(data.merged,Accession, GeneID = gID_D1,UniquePeps,MissingVal)
data.merged<-na.omit(data.merged)
} else {
tempdat$Accession <- tempdat[,input$accession]
if(input$genefile == FALSE){
uniGene <- uniprotGene()
# uniGene<- as.data.frame(uniGene,stringsAsFactors = FALSE)
#uniGene$Gene.names <- gsub(' .*','',uniGene$Gene.names)
print(head(uniGene))
} else{
uniGene <- uploadGene()
colnames(uniGene)[1:2] <- c('Entry','Gene.names')
}
uniGene$Gene.names[uniGene$Gene.names == '']<- NA
GeneID <- uniGene$Gene.names[match(tempdat$Accession,uniGene$Entry)]
GeneID <- make.names(GeneID,unique = TRUE)
print(GeneID)
Accession <- tempdat$Accession
UniquePeps <- MissingVal<- tempdat[,input$unipeps]
# data_orig2$geneID <- GeneID
data.merged <- cbind(data.merged,Accession, GeneID = GeneID,UniquePeps,MissingVal)
data.merged<-na.omit(data.merged)
print(head(data.merged))
}
missing<- rowSums(is.na(data.merged[,channels()]))
missing_val <- 0
data.merged$MissingVal <- missing
## subset by missing
data.merged <- data.merged[data.merged$MissingVal <= missing_val, ]
data.merged<- as.data.frame(data.merged[data.merged$MissingVal <= missing_val, ])
data.merged <- data.merged[data.merged$UniquePeps > 1, ]
data.merged<-na.omit(data.merged)
#
#
if(input$normalize == 'loess'){
data.merged <- data.frame(log2(normalize.loess(2^(data.merged[,channels()]))),
Accession=data.merged$Accession,
GeneID=data.merged$GeneID,
UniquePeps=data.merged$UniquePeps,
MissingVal=data.merged$MissingVal)
}else if(input$normalize == 'median'){
data.merged <- data.frame(log2( sweep( (2^(data.merged[,channels()]) ) ,
MARGIN = 2,
as.numeric(apply((2^(data.merged[,channels()])),2,median)),
FUN = "/")
),
Accession=data.merged$Accession,
GeneID=data.merged$GeneID,
UniquePeps=data.merged$UniquePeps,
MissingVal=data.merged$MissingVal)
}else{
data.merged <- data.frame(log2((2^(data.merged[,channels()]))),
Accession=data.merged$Accession,
GeneID=data.merged$GeneID,
UniquePeps=data.merged$UniquePeps,
MissingVal=data.merged$MissingVal)
}
data.merged<-na.omit(data.merged)
data.merged
## filter for 2 unique peptide
}
} else {
### intensities to protein done.. here no description so we need toi use accession and intermine
tempdat <- inten
if(input$genefile == FALSE){
uniGene <- uniprotGene()
#uniGene$Gene.names <- gsub(' .*','',uniGene$Gene.names)
}else{
uniGene <- uploadGene()
colnames(uniGene) <- c('Entry','Gene.names')
}
if(input$dorem =='yes'){
Accession <- tempdat$pepsum1.Accession
}else{
Accession <- tempdat$Accession
}
uniGene$Gene.names[uniGene$Gene.names == '']<- NA
GeneID <- uniGene$Gene.names[match(Accession,uniGene$Entry)]
GeneID <- make.names(GeneID,unique = TRUE)
tempdat$GeneID <- GeneID
UniquePeps <- tempdat$uniquePepr1
if(input$reps == 1){
data.merged <- tempdat
final.Names <- paste0('rep1_C',0:(input$chans - 2))
if(input$incpd == TRUE){
data.merged <- data.frame(data.merged[,1:(input$chans -1 )], Accession = data.merged$Accession,
GeneID = data.merged$GeneID, UniquePeps = data.merged$uniquePepr1, Kd = data.merged$Kd)
colnames(data.merged)<- c(final.Names,
"Accession", "GeneID","UniquePeps", 'Kd')
tmp<-data.merged[,1:(input$chans -1 )]
tf <- as.data.frame(lapply(tmp, function(x) (is.na(x))))
countsNAs<-as.data.frame(apply(tf,1,function(x)table(x)["TRUE"]))
n_of_miss<-as.data.frame(as.numeric(str_replace_all(as.list(countsNAs[,1]),"NA",'0')))
data.merged <- data.frame(data.merged,n_of_miss)
colnames(data.merged)<-c( final.Names,
"Accession", "GeneID","UniquePeps",'Kd',"MissingVal")
#
missing_val <- 0
#
data.merged<- as.data.frame(data.merged[data.merged$MissingVal <= missing_val, ])
#
# #Specify the number of missing points.For zero missing point is ==0
#
# #filiter for 2 unique peptides
data.merged <- data.merged[data.merged$UniquePeps > 1, ]
#
#
if(input$normalize == 'loess'){
data.merged <- data.frame(log2(normalize.loess(2^(data.merged[,1:(input$chans -1)]))),
Accession=data.merged$Accession,
GeneID=data.merged$GeneID,
UniquePeps=data.merged$UniquePeps,
Kd = data.merged$Kd
)
}else if(input$normalize == 'median'){
data.merged <- data.frame(log2( sweep( (2^(data.merged[,1:(input$chans -1)]) ) ,
MARGIN = 2,
as.numeric(apply((2^(data.merged[,1:(input$chans -1)])),2,median)),
FUN = "/")
),
Accession=data.merged$Accession,
GeneID=data.merged$GeneID,
UniquePeps=data.merged$UniquePeps,
Kd = data.merged$Kd
)
}else{
data.merged <- data.frame(log2(2^(data.merged[,1:(input$chans -1)])),
Accession=data.merged$Accession,
GeneID=data.merged$GeneID,
UniquePeps=data.merged$UniquePeps,
Kd = data.merged$Kd
)
}
data.merged<-na.omit(data.merged)
data.merged
} else {
data.merged <- data.frame(data.merged[,1:(input$chans -1 )], Accession = data.merged$Accession,
GeneID = data.merged$GeneID, UniquePeps = data.merged$uniquePepr1)
colnames(data.merged)<- c(final.Names,
"Accession", "GeneID","UniquePeps")
tmp<-data.merged[,1:(input$chans -1 )]
tf <- as.data.frame(lapply(tmp, function(x) (is.na(x))))
countsNAs<-as.data.frame(apply(tf,1,function(x)table(x)["TRUE"]))
n_of_miss<-as.data.frame(as.numeric(str_replace_all(as.list(countsNAs[,1]),"NA",'0')))
data.merged <- data.frame(data.merged,n_of_miss)
colnames(data.merged)<-c( final.Names,
"Accession", "GeneID","UniquePeps","MissingVal")
#
missing_val <- 0
#
data.merged<- as.data.frame(data.merged[data.merged$MissingVal <= missing_val, ])
#
# #Specify the number of missing points.For zero missing point is ==0
#
# #filiter for 2 unique peptides
data.merged <- data.merged[data.merged$UniquePeps > 1, ]
#
#
if(input$normalize == 'loess'){
data.merged <- data.frame(log2(normalize.loess(2^(data.merged[,1:(input$chans -1)]))),
Accession=data.merged$Accession,
GeneID=data.merged$GeneID,
UniquePeps=data.merged$UniquePeps)
}else if(input$normalize == 'median'){
data.merged <- data.frame(log2( sweep( (2^(data.merged[,1:(input$chans -1)]) ) ,
MARGIN = 2,
as.numeric(apply((2^(data.merged[,1:(input$chans -1)])),2,median)),
FUN = "/")
),
Accession=data.merged$Accession,
GeneID=data.merged$GeneID,
UniquePeps=data.merged$UniquePeps)
}else{
data.merged <- data.frame(log2(((2^(data.merged[,1:(input$chans -1)])))),
Accession=data.merged$Accession,
GeneID=data.merged$GeneID,
UniquePeps=data.merged$UniquePeps)
}
data.merged<-na.omit(data.merged)
data.merged
}
} else{
data.merged <- tempdat[,1:(input$chans*input$reps - 2)]
data.merged <- tempdat[,1:(input$chans*input$reps - 2)]
if( input$dorem == 'no'){
Accession <- tempdat$Accession
MissingVal <- UniquePeps
data.merged <- cbind(data.merged,Accession, GeneID = GeneID,UniquePeps,MissingVal)
data.merged <- data.merged[!is.na(rowSums(data.merged[,1:(input$chans*input$reps -2)])),]
#PR add the na.omit
data.merged <- na.omit(data.merged[data.merged$UniquePeps > 1, ])
if(input$normalize == 'loess'){
data.merged <- data.frame((log2(normalize.loess(2^(data.merged[,1:(input$chans*input$reps - 2)])))),
Accession=data.merged$Accession,
GeneID=data.merged$GeneID,
UniquePeps=data.merged$UniquePeps)
}else if(input$normalize == 'median'){
data.merged <- data.frame(log2( sweep( (2^(data.merged[,1:(input$chans*input$reps - 2)]) ) ,
MARGIN = 2,
as.numeric(apply((2^(data.merged[,1:(input$chans*input$reps - 2)])),2,median)),
FUN = "/")
),
Accession=data.merged$Accession,
GeneID=data.merged$GeneID,
UniquePeps=data.merged$UniquePeps)
}else{
data.merged <- data.frame((log2((2^(data.merged[,1:(input$chans*input$reps - 2)])))),
Accession=data.merged$Accession,
GeneID=data.merged$GeneID,
UniquePeps=data.merged$UniquePeps)
}
data.merged <- data.merged[!is.na(rowSums(data.merged[,1:(input$chans*input$reps -2)])),]
data.merged<-na.omit(data.merged)
data.merged
}else{
Accession <- tempdat$pepsum1.Accession
data.merged <- cbind(data.merged,Accession, GeneID = GeneID,UniquePeps, num1 = tempdat$num1, num2 = tempdat$num2)
data.merged <- data.merged[!is.na(rowSums(data.merged[,1:(input$chans*input$reps -2)])),]
#PR add the na.omit
data.merged <- na.omit(data.merged[data.merged$UniquePeps > 1, ])
if(input$normalize == 'loess'){
data.merged <- data.frame((log2(normalize.loess(2^(data.merged[,1:(input$chans*input$reps - 2)])))),
Accession=data.merged$Accession,
GeneID=data.merged$GeneID,
UniquePeps=data.merged$UniquePeps, num1 = data.merged$num1, num2 = data.merged$num2)
}else if(input$normalize == 'median'){
data.merged <- data.frame(log2( sweep( (2^(data.merged[,1:(input$chans*input$reps - 2)]) ) ,
MARGIN = 2,
as.numeric(apply((2^(data.merged[,1:(input$chans*input$reps - 2)])),2,median)),
FUN = "/")
),
Accession=data.merged$Accession,
GeneID=data.merged$GeneID,
UniquePeps=data.merged$UniquePeps, num1 = data.merged$num1, num2 = data.merged$num2)
}else{
data.merged <- data.frame((log2((2^(data.merged[,1:(input$chans*input$reps - 2)])))),
Accession=data.merged$Accession,
GeneID=data.merged$GeneID,
UniquePeps=data.merged$UniquePeps, num1 = data.merged$num1, num2 = data.merged$num2)
}
data.merged <- data.merged[data.merged$num1 > 1 | data.merged$num2 > 1 , ]
data.merged <- data.merged[!is.na(rowSums(data.merged[,1:(input$chans*input$reps -2)])),]
data.merged<-na.omit(data.merged)
data.merged
}
}
}
data.merged<-na.omit(data.merged)
data.merged
})
sigFinalNames <- reactive({
paste0("C_",1:input$chans)
})
sigPredNames <- reactive({
paste0("predX",1:input$chans)
})
dataMerge2 <- reactive({
nvec <- channels()
nvec <- length(nvec)
data.merged <- dataMerge()
if(input$modtyp == "sigmoid"){
if(input$datype == 'intensity'){
conc <- sigConc()
if(input$incpd == TRUE){
final.Names <- paste0('rep1_C',0:(input$chans - 2 ))
pred.names <- paste0('predX',1:(input$chans -1))
colnames(data.merged[,1:(input$chans -1)]) <- final.Names
data_merged_positives<- data.merged
data.merged<-na.omit(data.merged[data.merged[,1:input$chans] >= 1,])
data_merged_positives2<-( (1/data_merged_positives[,1:(input$chans -1 )]))*100
Reps_FC<-data.frame(data_merged_positives2 ,
Accession = data_merged_positives$Accession,GeneID = data_merged_positives$GeneID,
UniquePeps = data_merged_positives$UniquePeps, depletionConstant = data_merged_positives$Kd
)
ryegrass.m1<- vector(mode = "list",length = nrow(Reps_FC))
pvals<-list()
stderr<-list()
model_pred<-list()
coeff_predicted<-list()
for(i in 1:nrow(Reps_FC)){
#print(i)
#nrow(full_df_2)
#maxIt and relTol to be user defined
ryegrass.m1[[i]]<-try(drm(as.numeric(Reps_FC[i,1:(input$chans - 1 )]) ~ as.numeric(conc),
na.action = na.omit,
control = drmc(constr = FALSE, errorm = FALSE, noMessage = TRUE, maxIt = 1000, relTol = 1e-06),
fct = LL.4(fixed=c(NA, NA, NA, NA), #see note @top this file
names = c("Slope", "Lower Limit", "Upper Limit", "RB50"))),silent = TRUE)
}
failed_sigm=0
for(i in 1:length(ryegrass.m1)){
#print(i)
#checking_val if FALSE the model has failed to calculate the pval
checking_val<-try(is.numeric(coefficients(ryegrass.m1[[i]])[["Slope:(Intercept)"]]),silent = TRUE)
if(checking_val=="TRUE"){
#print(checking_val)
pvals[[i]]<-t(as.data.frame(summary(ryegrass.m1[[i]])$coefficients[13:16]))
colnames(pvals[[i]])<-c("SlopePval", "Lower_LimitPval", "Upper_LimitPval", "RB50Pval")
coeff_predicted[[i]]<-t(data.frame(coefficients(ryegrass.m1[[i]])))
colnames(coeff_predicted[[i]])<-c("SlopeCoef", "Lower_LimitCoef", "Upper_LimitCoef","RB50Coef")
stderr[[i]]<-t(as.data.frame(summary(ryegrass.m1[[i]])$coefficients[5:8]))
colnames(stderr[[i]])<-c("SlopeErr", "Lower_LimitErr", "Upper_LimitErr","RB50Err")
model_pred[[i]]<-predict(ryegrass.m1[[i]])
}else{
failed_sigm=failed_sigm+1
fit <- lm(as.numeric(Reps_FC[i,1:(input$chans -1)]) ~ poly(log10(conc),2 ))
#extract the pval
pval<-as.numeric(summary(fit)$coefficients[,4] )
pvals[[i]]<- t(as.data.frame(c(pval,"lm-fit:intercept.slope.quadratic") ))
colnames(pvals[[i]])<-c("SlopePval", "Lower_LimitPval", "Upper_LimitPval","RB50Pval")
stderr[[i]]<- data.frame(NA,NA,NA,NA)
colnames(stderr[[i]])<-c("SlopeErr", "Lower_LimitErr", "Upper_LimitErr","RB50Err")
coeff_predicted[[i]]<-data.frame(NA,NA,NA,NA)
colnames(coeff_predicted[[i]])<-c("SlopeCoef", "Lower_LimitCoef", "Upper_LimitCoef","RB50Coef")
model_pred[[i]]<- as.numeric(fitted(fit))
} #just adding NAs for the times the model failed
}
modelsReps<-data.frame(
do.call(rbind.data.frame,lapply(model_pred,function(x) as.numeric(x))),
Reps_FC$GeneID,
do.call(rbind.data.frame,lapply(pvals,function(x) x) ),
do.call(rbind.data.frame,lapply(coeff_predicted,function(x) x)) ,
do.call(rbind.data.frame,lapply(stderr,function(x) x) )
)
colnames(modelsReps)<-c(pred.names,"GeneID",
"SlopePval", "Lower_LimitPval","Upper_LimitPval", "RB50Pval",
"SlopeCoef", "Lower_LimitCoef","Upper_LimitCoef", "RB50Coef",
"SlopeErr", "Lower_LimitErr","Upper_LimitErr", "RB50Err"
)
data_merged_2 <-merge.data.frame(modelsReps,Reps_FC,by = 'GeneID')
data_merged_2<-data.frame(data_merged_2,"Top_minus_min"=data_merged_2$predX1-data_merged_2[,paste("predX",(input$chans-1),sep = "")])
crap <- crapome()
#
tempcrap <- crap$Gene
tempcrap<- crap$percentagePresent[match(data_merged_2$GeneID,crap$Gene)]
data_merged_2 <- data.frame(data_merged_2, CRAPomePercent = tempcrap)
proteome<-as.vector(toupper(data_merged_2$GeneID))
mykinases <- intersect(proteome,kinome)
if(!is.null(input$venninp)){
myvenninp <- uploadVenn()
uploadsInt <- intersect(proteome,myvenninp)
myvenvec <- match(proteome, uploadsInt, nomatch = NA)
## now combine with my kin vec
mykinvec <- match(proteome,mykinases, nomatch = NA)
mykinvec[!is.na(mykinvec) & !is.na(myvenvec)] <- 'KINASE + UPLOAD'
mykinvec[!is.na(mykinvec) & is.na(myvenvec)] <- 'KINASE'
mykinvec[is.na(mykinvec) & !is.na(myvenvec)] <- 'UPLOAD'
print(mykinvec)
} else {
mykinvec <- match(proteome,mykinases, nomatch = NA)
mykinvec[!is.na(mykinvec)]<- 'KINASE'
}
data_merged_2<- data.frame(data_merged_2, correctedRB50 = (data_merged_2$RB50Coef*data_merged_2$depletionConstant),Kinase = mykinvec)
data_merged_2
} else {
final.Names <- paste0('rep1_C',0:(input$chans - 2 ))
pred.names <- paste0('predX',1:(input$chans -1))
colnames(data.merged[,1:(input$chans -1)]) <- final.Names
data_merged_positives<- data.merged
# na.omit(data.merged[data.merged[,1:input$chans] >= 1,])
data_merged_positives2<-( (1/data_merged_positives[,1:(input$chans -1 )]))*100
Reps_FC<-data.frame(data_merged_positives2 ,
Accession = data_merged_positives$Accession,GeneID = data_merged_positives$GeneID,
UniquePeps = data_merged_positives$UniquePeps
)
ryegrass.m1<- vector(mode = "list",length = nrow(Reps_FC))
pvals<-list()
stderr<-list()
model_pred<-list()
coeff_predicted<-list()
for(i in 1:nrow(Reps_FC)){
#print(i)
#nrow(full_df_2)
#maxIt and relTol to be user defined
ryegrass.m1[[i]]<-try(drm(as.numeric(Reps_FC[i,1:(input$chans - 1 )]) ~ as.numeric(conc),
na.action = na.omit,
control = drmc(constr = FALSE, errorm = FALSE, noMessage = TRUE, maxIt = 1000, relTol = 1e-06),
fct = LL.4(fixed=c(NA, NA, NA, NA), #see note @top this file
names = c("Slope", "Lower Limit", "Upper Limit", "RB50"))),silent = TRUE)
}
failed_sigm=0
for(i in 1:length(ryegrass.m1)){
#print(i)
#checking_val if FALSE the model has failed to calculate the pval
checking_val<-try(is.numeric(coefficients(ryegrass.m1[[i]])[["Slope:(Intercept)"]]),silent = TRUE)
if(checking_val=="TRUE"){
#print(checking_val)
pvals[[i]]<-t(as.data.frame(summary(ryegrass.m1[[i]])$coefficients[13:16]))
colnames(pvals[[i]])<-c("SlopePval", "Lower_LimitPval", "Upper_LimitPval", "RB50Pval")
coeff_predicted[[i]]<-t(data.frame(coefficients(ryegrass.m1[[i]])))
colnames(coeff_predicted[[i]])<-c("SlopeCoef", "Lower_LimitCoef", "Upper_LimitCoef","RB50Coef")
stderr[[i]]<-t(as.data.frame(summary(ryegrass.m1[[i]])$coefficients[5:8]))
colnames(stderr[[i]])<-c("SlopeErr", "Lower_LimitErr", "Upper_LimitErr","RB50Err")
model_pred[[i]]<-predict(ryegrass.m1[[i]])
}else{
failed_sigm=failed_sigm+1
fit <- lm(as.numeric(Reps_FC[i,1:(input$chans -1)]) ~ poly(log10(conc),2 ))
#extract the pval
pval<-as.numeric(summary(fit)$coefficients[,4] )
pvals[[i]]<- t(as.data.frame(c(pval,"lm-fit:intercept.slope.quadratic") ))
colnames(pvals[[i]])<-c("SlopePval", "Lower_LimitPval", "Upper_LimitPval","RB50Pval")
stderr[[i]]<- data.frame(NA,NA,NA,NA)
colnames(stderr[[i]])<-c("SlopeErr", "Lower_LimitErr", "Upper_LimitErr","RB50Err")
coeff_predicted[[i]]<-data.frame(NA,NA,NA,NA)
colnames(coeff_predicted[[i]])<-c("SlopeCoef", "Lower_LimitCoef", "Upper_LimitCoef","RB50Coef")
model_pred[[i]]<- as.numeric(fitted(fit))
} #just adding NAs for the times the model failed
}
modelsReps<-data.frame(
do.call(rbind.data.frame,lapply(model_pred,function(x) as.numeric(x))),
Reps_FC$GeneID,
do.call(rbind.data.frame,lapply(pvals,function(x) x) ),
do.call(rbind.data.frame,lapply(coeff_predicted,function(x) x)) ,
do.call(rbind.data.frame,lapply(stderr,function(x) x) )
)
colnames(modelsReps)<-c(pred.names,"GeneID",
"SlopePval", "Lower_LimitPval","Upper_LimitPval", "RB50Pval",
"SlopeCoef", "Lower_LimitCoef","Upper_LimitCoef", "RB50Coef",
"SlopeErr", "Lower_LimitErr","Upper_LimitErr", "RB50Err"
)
data_merged_2 <-merge.data.frame(modelsReps,Reps_FC,by = 'GeneID')
data_merged_2<-data.frame(data_merged_2,"Top_minus_min"=data_merged_2$predX1-data_merged_2[,paste("predX",(input$chans-1),sep = "")])
## crapome integration
crap <- crapome()
#
tempcrap <- crap$Gene
tempcrap<- crap$percentagePresent[match(data_merged_2$GeneID,crap$Gene)]
data_merged_2 <- data.frame(data_merged_2, CRAPomePercent = tempcrap)
proteome<-as.vector(toupper(data_merged_2$GeneID))
mykinases <- intersect(proteome,kinome)
if(!is.null(input$venninp)){
myvenninp <- uploadVenn()
uploadsInt <- intersect(proteome,myvenninp)
myvenvec <- match(proteome, uploadsInt, nomatch = NA)
## now combine with my kin vec
mykinvec <- match(proteome,mykinases, nomatch = NA)
mykinvec[!is.na(mykinvec) & !is.na(myvenvec)] <- 'KINASE + UPLOAD'
mykinvec[!is.na(mykinvec) & is.na(myvenvec)] <- 'KINASE'
mykinvec[is.na(mykinvec) & !is.na(myvenvec)] <- 'UPLOAD'
print(mykinvec)
} else {
mykinvec <- match(proteome,mykinases, nomatch = NA)
mykinvec[!is.na(mykinvec)]<- 'KINASE'
}
data_merged_2<- data.frame(data_merged_2,Kinase = mykinvec)
data_merged_2
}
} else{
conc <- sigConc()
final.Names <- sigFinalNames()
pred.names <- sigPredNames()
colnames(data.merged[,1:input$chans]) <- final.Names
data_merged_positives<- data.merged
# na.omit(data.merged[data.merged[,1:input$chans] >= 1,])
data_merged_positives2<-( (1/data_merged_positives[,1:input$chans]))*100
if(input$incpd == TRUE){
Reps_FC<-data.frame(data_merged_positives2 ,
Accession = data_merged_positives$Accession,GeneID = data_merged_positives$GeneID,
UniquePeps = data_merged_positives$UniquePeps, depletionConstant = data_merged_positives$Kd, MissingVal = data_merged_positives$MissingVal
)
}else{
Reps_FC<-data.frame(data_merged_positives2 ,
Accession = data_merged_positives$Accession,GeneID = data_merged_positives$GeneID,
UniquePeps = data_merged_positives$UniquePeps, MissingVal = data_merged_positives$MissingVal
)
}
ryegrass.m1<- vector(mode = "list",length = nrow(Reps_FC))
pvals<-list()
stderr<-list()
model_pred<-list()
coeff_predicted<-list()
for(i in 1:nrow(Reps_FC)){
#print(i)
#nrow(full_df_2)
#maxIt and relTol to be user defined
ryegrass.m1[[i]]<-try(drm(as.numeric(Reps_FC[i,1:input$chans]) ~ as.numeric(conc),
na.action = na.omit,
control = drmc(constr = FALSE, errorm = FALSE, noMessage = TRUE, maxIt = 1000, relTol = 1e-06),
fct = LL.4(fixed=c(NA, NA, NA, NA), #see note @top this file
names = c("Slope", "Lower Limit", "Upper Limit", "RB50"))),silent = TRUE)
}
failed_sigm=0
for(i in 1:length(ryegrass.m1)){
#print(i)
#checking_val if FALSE the model has failed to calculate the pval
checking_val<-try(is.numeric(coefficients(ryegrass.m1[[i]])[["Slope:(Intercept)"]]),silent = TRUE)
if(checking_val=="TRUE"){
#print(checking_val)
pvals[[i]]<-t(as.data.frame(summary(ryegrass.m1[[i]])$coefficients[13:16]))
colnames(pvals[[i]])<-c("SlopePval", "Lower_LimitPval", "Upper_LimitPval", "RB50Pval")
coeff_predicted[[i]]<-t(data.frame(coefficients(ryegrass.m1[[i]])))
colnames(coeff_predicted[[i]])<-c("SlopeCoef", "Lower_LimitCoef", "Upper_LimitCoef","RB50Coef")
stderr[[i]]<-t(as.data.frame(summary(ryegrass.m1[[i]])$coefficients[5:8]))
colnames(stderr[[i]])<-c("SlopeErr", "Lower_LimitErr", "Upper_LimitErr","RB50Err")
model_pred[[i]]<-predict(ryegrass.m1[[i]])
}else{
failed_sigm=failed_sigm+1
fit <- lm(as.numeric(Reps_FC[i,1:input$chans]) ~ poly(log10(conc),2 ))
#extract the pval
pval<-as.numeric(summary(fit)$coefficients[,4] )
pvals[[i]]<- t(as.data.frame(c(pval,"lm-fit:intercept.slope.quadratic") ))
colnames(pvals[[i]])<-c("SlopePval", "Lower_LimitPval", "Upper_LimitPval","RB50Pval")
stderr[[i]]<- data.frame(NA,NA,NA,NA)
colnames(stderr[[i]])<-c("SlopeErr", "Lower_LimitErr", "Upper_LimitErr","RB50Err")
coeff_predicted[[i]]<-data.frame(NA,NA,NA,NA)
colnames(coeff_predicted[[i]])<-c("SlopeCoef", "Lower_LimitCoef", "Upper_LimitCoef","RB50Coef")
model_pred[[i]]<- as.numeric(fitted(fit))
} #just adding NAs for the times the model failed
}
modelsReps<-data.frame(
do.call(rbind.data.frame,lapply(model_pred,function(x) as.numeric(x))),
Reps_FC$GeneID,
do.call(rbind.data.frame,lapply(pvals,function(x) x) ),
do.call(rbind.data.frame,lapply(coeff_predicted,function(x) x)) ,
do.call(rbind.data.frame,lapply(stderr,function(x) x) )
)
colnames(modelsReps)<-c(pred.names,"GeneID",
"SlopePval", "Lower_LimitPval","Upper_LimitPval", "RB50Pval",
"SlopeCoef", "Lower_LimitCoef","Upper_LimitCoef", "RB50Coef",
"SlopeErr", "Lower_LimitErr","Upper_LimitErr", "RB50Err"
)
data_merged_2<-merge.data.frame(modelsReps,Reps_FC,by="GeneID")
data_merged_2<-data.frame(data_merged_2,"Top_minus_min"=data_merged_2$predX1-data_merged_2[,paste("predX",input$chans,sep = "")])
## crapome integration
crap <- crapome()
#
tempcrap <- crap$Gene
tempcrap<- crap$percentagePresent[match(data_merged_2$GeneID,crap$Gene)]
data_merged_2 <- data.frame(data_merged_2, CRAPomePercent = tempcrap)
proteome<-as.vector(toupper(data_merged_2$GeneID))
mykinases <- intersect(proteome,kinome)
if(!is.null(input$venninp)){
myvenninp <- uploadVenn()
uploadsInt <- intersect(proteome,myvenninp)
myvenvec <- match(proteome, uploadsInt, nomatch = NA)
## now combine with my kin vec
mykinvec <- match(proteome,mykinases, nomatch = NA)
mykinvec[!is.na(mykinvec) & !is.na(myvenvec)] <- 'KINASE + UPLOAD'
mykinvec[!is.na(mykinvec) & is.na(myvenvec)] <- 'KINASE'
mykinvec[is.na(mykinvec) & !is.na(myvenvec)] <- 'UPLOAD'
print(mykinvec)
} else {
mykinvec <- match(proteome,mykinases, nomatch = NA)
mykinvec[!is.na(mykinvec)]<- 'KINASE'
}
if(input$incpd == TRUE){
data_merged_2<- data.frame(data_merged_2, correctedRB50 = (data_merged_2$RB50Coef*data_merged_2$depletionConstant),Kinase = mykinvec)
}else{
data_merged_2<- data.frame(data_merged_2,Kinase = mykinvec)
}
data_merged_2
}
} else{
if(input$datype == "intensity"){
conc<- rep(0:(input$chans - 2), times = input$reps)
}else{
conc<- rep(0:(input$chans - 1), times = rReps())[channels()]
}
design<-model.matrix(~poly(conc,2))
colnames(design)<-c("Intercept","Slope","Quadratic")
# reactive start
fit <- lmFit(data.merged[,1:length(conc)], method = "ls" , design = design )
fit <- eBayes(fit)
res <- topTable(fit, coef = "Slope", number = nrow(data.merged), adjust="BH") #pval for the slope
res2 <- topTable(fit, coef = 1, number = nrow(data.merged), adjust="BH")#pval for the intercept
res3 <- topTable(fit, coef = "Quadratic", number = nrow(data.merged), adjust="BH") #pval for the quadratic term ()
#add the pvalues to the dataframe
tmp_1<- cbind(data.merged[rownames(res),],res)
tmp_2<- cbind(data.merged[rownames(res2),],res2)
tmp_3<- cbind(data.merged[rownames(res3),],res3)
####
tobeselected <- merge.data.frame(tmp_1,tmp_2,by="Accession")
tobeselected <- merge.data.frame(tobeselected,tmp_3,by="Accession")
print(colnames(tobeselected))
selectnames <- c(paste0(colnames(data.merged)[1:length(conc)],".x"),
"logFC.x", "AveExpr.x", "P.Value", "adj.P.Val", "P.Value.x",
"adj.P.Val.x", "P.Value.y", "adj.P.Val.y","Accession","GeneID.x","UniquePeps")
data.merged<- tobeselected[,match(selectnames, colnames(tobeselected))]
print(colnames(data.merged))
proteome<-as.vector(toupper(tobeselected$GeneID.x))
mykinases <- intersect(proteome,kinome)
if(!is.null(input$venninp)){
myvenninp <- uploadVenn()
uploadsInt <- intersect(proteome,myvenninp)
myvenvec <- match(proteome, uploadsInt, nomatch = NA)
## now combine with my kin vec
mykinvec <- match(proteome,mykinases, nomatch = NA)
mykinvec[!is.na(mykinvec) & !is.na(myvenvec)] <- 'KINASE + UPLOAD'
mykinvec[!is.na(mykinvec) & is.na(myvenvec)] <- 'KINASE'
mykinvec[is.na(mykinvec) & !is.na(myvenvec)] <- 'UPLOAD'
print(mykinvec)
} else {
mykinvec <- match(proteome,mykinases, nomatch = NA)
mykinvec[!is.na(mykinvec)]<- 'KINASE'
}
crap <- crapome()
#
tempcrap <- crap$Gene
tempcrap<- crap$percentagePresent[match(toupper(data.merged$GeneID.x),crap$Gene)]
data.merged <- data.frame(data.merged, CRAPomePercent = tempcrap,Kinase = mykinvec)
print(colnames(data.merged))
nam <- finalNames()
if(input$datype == 'intensity'){
nam <- nam[-seq(1,input$reps*input$chans,by = input$chans)]
}
colnames(data.merged)[1:length(nam)] <- nam
# print(colnames(data.merged[match(c('P.Value', 'adj.P.Val', 'P.Value.x', 'adj.P.Val.x', 'P.Value.y', 'adj.P.Val.y'),colnames(data.merged))]))
# colnames(data.merged[,match(c('P.Value', 'adj.P.Val', 'P.Value.x', 'adj.P.Val.x', 'P.Value.y', 'adj.P.Val.y'),colnames(data.merged))]) <- c('P.Value_intercept', 'adj.P.Val_intercept', 'P.Value_slope', 'adj.P.Val_slope', 'P.Value_quadratic', 'adj.P.Val_quadratic')
# colnames(data.merged[match(c('P.Value', 'adj.P.Val', 'P.Value.x', 'adj.P.Val.x', 'P.Value.y', 'adj.P.Val.y'),colnames(data.merged))]) <- c('P.Value_intercept', 'adj.P.Val_intercept', 'P.Value_slope', 'adj.P.Val_slope', 'P.Value_quadratic', 'adj.P.Val_quadratic')
data.merged
}
})
rSu<- reactive({
if(input$reps == 1 ){
data.merged<- dataMerge()
data.merged
}else{
data.merged <- dataMerge2()
data.merged
}
})
###################
## output
###################
output$venn <- renderPlot({
req(data())
if(!is.null(input$venninp)){
upload <- uploadVenn()
upload<- as.vector(toupper(upload))
print(upload)
data.merged <- dataMerge()
proteome<-as.vector(toupper(data.merged$GeneID))
universe <- unique(c(kinome,proteome,upload))
count<- matrix(0, ncol = 3 , nrow = length(universe))
colnames(count) <- c("kinome",'proteome','upload')
for(i in 1:length(universe)){
count[i,1]<- universe[i] %in% kinome
count[i,2]<- universe[i] %in% proteome
count[i,3]<- universe[i] %in% upload
}
vennDiagram(vennCounts(count), circle.col = c("blue","red","green"), cex = 1,lwd = 2)
}else{
data.merged <- dataMerge()
proteome<-as.vector(toupper(data.merged$GeneID))
universe <- unique(c(kinome,proteome))
# Generate a matrix, with the sets in columns and possible letters on rows
Counts <- matrix(0, nrow=length(universe), ncol=2)
# Populate the said matrix
for (i in 1:length(universe)) {
Counts[i,1] <- universe[i] %in% kinome
Counts[i,2] <- universe[i] %in% proteome
#Counts[i,3] <- universe[i] %in% Metacore
#Counts[i,3] <- universe[i] %in% EXOCYTOSIS
}
colnames(Counts) <- c("Kinome","Proteome")
cols<-c("Red", "Blue")
#### VENN
vennDiagram(vennCounts(Counts), circle.col=cols,
cex=1, #title size
lwd=2 #circle line size
)
}
})
output$bar<- renderPlot({
vec<- channels()
vec<- length(vec)
palette.bar <- rep(terrain.colors(input$reps),each = ifelse(input$datype != 'intensity',input$chans,input$chans - 1 ) )
data.merged<- dataMerge()
boxplot(data.merged[,1:vec], col=palette.bar,las=2, cex.axis=1, main=c("Box Plots"),
ylab=c("Log2(ratios)"))
legend("topright",legend = paste("rep",1:input$reps,sep = ' '), fill = terrain.colors(input$reps))
})
output$plot2<-renderPlot({
vec <- channels()
pal <- rainbow(length(vec))
leg.nam <- finalNames()
data.merged <- dataMerge()
missing_val <- 0
par(mfrow = c(1,2))
plot(x=rank(data.merged[,1]),y=data.merged[,1], cex.axis=1,
main=c("Change Distribution"),
col=pal[1], ylab=c("Log2(ratios)"), xlab = c("Proteins"))
if(length(vec) > 1){
for(i in 2:length(vec)){
points(x=rank(data.merged[,i]),y=data.merged[,i], cex.axis=1, main=c(""),col=pal[i])
}
}
legend("topleft", legend = leg.nam, fill = pal)
plot(density(x=data.merged[,1]),col= pal[1], main=c(" Density Distribution"), ylim = c(0,5 ),cex.axis = 1)
legend("topleft", legend = leg.nam, fill = pal)
if(length(vec) > 1){
for(i in 2:length(vec)){
lines(density(x=data.merged[,i]), col=pal[i], main = c(""))
}
}
})
output$plot3<- renderPlot({
vec <- channels()
data.merged<- dataMerge()
# print(colnames(data.merged))
vsn::meanSdPlot(as.matrix(data.merged[,1:length(vec)]))
})
output$plot4<- renderPlot({
if(input$modtyp == 'sigmoid'){
plot.new()
legend('topleft', c("Sigmoidal fit applied, no linear plots available"),bty = 'n')
}else{
data.merged<- dataMerge2()
m0 <- ggplot(data.merged, aes(x=data.merged$P.Value))
m0<-m0 + geom_histogram(aes(fill = ..count..),binwidth = 0.01) +
scale_fill_gradient("Count", low = "green", high = "red")+
xlab("P.val slope")
m1 <- ggplot(data.merged, aes(x=data.merged$P.Value.x))
m1<- m1 + geom_histogram(aes(fill = ..count..),binwidth = 0.01) +
scale_fill_gradient("Count", low = "green", high = "red")+
xlab("Pval intercept")
m2 <- ggplot(data.merged, aes(x=data.merged$P.Value.y))
m2 <- m2 + geom_histogram(aes(fill = ..count..),binwidth = 0.01) +
scale_fill_gradient("Count", low = "green", high = "red")+
xlab("Pval quadratic")
grid.arrange(m0,m1,m2)
}
})
output$volcanoint<- renderPlot({
res<- dataMerge2()
# avgthr=0.2 #sign threshold for the averege fold change 0.3(log2) is 1.3 FC
par(mar=c(5,5,5,10), xpd=TRUE)
# Make a basic volcano plot
with(res, plot(res$AveExpr.x, -log10(res$P.Value.x), pch=20, main="Volcano plot (Intercept pval )",xlab=c("Log2_AvgFC"),ylab=c("-Log10(Pval)"), xlim=c(-abs(max(res$AveExpr.x)+1),abs(max(res$AveExpr.x)+1))))
# Add colored points: red if padj<0.05, orange of log2FC>1, green if both)
s=subset(res, P.Value.x<input$pvalsli )
with(s, points(s$AveExpr.x, -log10(s$P.Value.x), pch=20, col="red"))
s=subset(res, abs(res$AveExpr.x)>input$avthrssli)
with(s, points(s$AveExpr.x, -log10(s$P.Value.x), pch=20, col="orange"))
s=subset(res, P.Value.x<input$pvalsli & abs(res$AveExpr.x)>input$avthrssli)
with(s, points(s$AveExpr.x, -log10(s$P.Value.x), pch=20, col="green"))
# Label points with the textxy function from the calibrate plot
s=subset(res, P.Value.x<input$pvalsli & abs(res$AveExpr.x)>input$avthrssli)
with(s, textxy( s$AveExpr.x, -log10(s$P.Value.x), labs=s$GeneID.x, cex=1)
)
legend("bottomleft", title="Legend",cex = 0.8,
c("Not significant",
paste("P.Value",input$pvalsli, sep = " "), #red
paste("AvgFC >", input$avthrssli, sep=""), #orange,
paste("P.Value", input$pvalsli,"& AvgFC >", input$avthrssli, sep="") #green
),
col=c("black","red","orange","green"),
horiz=FALSE, pch=c(19))
})
output$volcanoquad<- renderPlot({
res<- dataMerge2()
# avgthr=0.2 #sign threshold for the averege fold change 0.3(log2) is 1.3 FC
par(mar=c(5,5,5,10), xpd=TRUE)
# Make a basic volcano plot
with(res, plot(res$AveExpr.x, -log10(res$P.Value.y), pch=20, main="Volcano plot (Quadratic pval )",xlab=c("Log2_AvgFC"),ylab=c("-Log10(Pval)"), xlim=c(-abs(max(res$AveExpr.x)+1),abs(max(res$AveExpr.x)+1))))
# Add colored points: red if padj<0.05, orange of log2FC>1, green if both)
s=subset(res, P.Value.y<input$pvalsli )
with(s, points(s$AveExpr.x, -log10(s$P.Value.y), pch=20, col="red"))
s=subset(res, abs(res$AveExpr.x)>input$avthrssli)
with(s, points(s$AveExpr.x, -log10(s$P.Value.y), pch=20, col="orange"))
s=subset(res, P.Value.y<input$pvalsli & abs(res$AveExpr.x)>input$avthrssli)
with(s, points(s$AveExpr.x, -log10(s$P.Value.y), pch=20, col="green"))
# Label points with the textxy function from the calibrate plot
s=subset(res, P.Value.y<input$pvalsli & abs(res$AveExpr.x)>input$avthrssli)
with(s, textxy( s$AveExpr.x, -log10(s$P.Value.y), labs=s$GeneID.x, cex=.9)
)
legend("bottomleft", title="Legend",cex = 0.7,
c("Not significant",
paste("P.Value",input$pvalsli, sep = " "), #red
paste("AvgFC >", input$avthrssli, sep=""), #orange,
paste("P.Value", input$pvalsli,"& AvgFC >", input$avthrssli, sep="") #green
),
col=c("black","red","orange","green"),
horiz=FALSE, pch=c(19))
})
output$repvsrep1 <- renderUI({
# a <- finalNames()
# a <- paste0(a,".x")
# b <- channels()
a<- indexmatrix()
selectizeInput(inputId = "repvsrep1",label = "Select Condition", choices = as.character(a$names), multiple = FALSE)
})
output$repvsrep2 <- renderUI({
a <- finalNames()
a <- paste0(a,".x")
b <- channels()
c <- a[b]
if(is.null(input$repvsrep1)){
e <- c
} else {
d <- match(input$repvsrep1,c)
e <- c[-d]
}
selectInput(inputId = "repvsrep2",label = "Select Condition", choices = e, multiple = FALSE)
})
output$repvsrep <- renderPlot({
if(input$reps > 1){
data.merged <- dataMerge2()
index <- indexmatrix()
val = max(c(max(data.merged[,index[index[,1] == input$repvsrep1,5]],na.rm = TRUE),max(data.merged[,index[index[,1] == input$repvsrep1,6]],na.rm = TRUE)))
plot(x=data.merged[,index[index[,1] == input$repvsrep1,5]],y=data.merged[,index[index[,1] == input$repvsrep1,6]], xlim=c(0,val +0.2), col="green" , ylim=c(0,val+0.2),
cex.axis=1.2, main=c("LogFC-LogFC Plots"),
xlab=paste("rep",index[index[,1] == input$repvsrep1,3]), ylab=paste("rep",index[index[,1] == input$repvsrep1,4]))
text(data.merged[,index[index[,1] == input$repvsrep1,5]], data.merged[,index[index[,1] == input$repvsrep1,6]], labels=data.merged$GeneID, cex= 1,pos=4)
lines(x = c(0,val), y = c(0,val),col="red")
} else {
plot.new()
title(main = 'Plot not available: only 1 replicate')
}
})
output$plot5<- renderPlot({
req(data())
if(input$modtyp == 'sigmoid'){
su <- dataMerge()
}else{
su<- rSu()
}
index<- channels()
index<- length(index)
cmat <-cor(su[,1:index],use="pairwise", method = "pearson")
corrgram(cmat, order=TRUE, lower.panel=panel.shadeNtext,
upper.panel=panel.pie, text.panel=panel.txt,
main="Corrgram Plots" )
})
### MeanDiff
output$meandiff1 <- renderUI({
a <- indexmatrix()
selectizeInput(inputId = "meandiff1",label = "Select Condition", choices = as.character(a$names), multiple = FALSE)
})
output$meandiff2 <- renderUI({
a <- finalNames()
a <- paste0(a,".x")
b <- channels()
c <- a[b]
if(is.null(input$meandiff1)){
e <- c
} else {
d <- match(input$meandiff1,c)
e <- c[-d]
}
selectInput(inputId = "meandiff2",label = "Select Condition", choices = e, multiple = FALSE)
})
output$plot6<- renderPlot({
req(data())
if(input$modtyp == 'sigmoid' | input$reps == 1){
plot.new()
title(main = 'Plot not available: only 1 replicate')
}else{
# data.merged <- dataMerge()
su <- rSu()
index <- indexmatrix()
minxy <- min(c(min(su[,index[index[,1] == input$meandiff1,5]]),min(su[,index[index[,1] == input$meandiff1,6]])))
maxxy <- max(c(max(su[,index[index[,1] == input$meandiff1,5]]),max(su[,index[index[,1] == input$meandiff1,6]])))
tmd(
xyplot(su[,index[index[,1] == input$meandiff1,5]] ~ su[,index[index[,1] == input$meandiff1,6]]), main=input$meandiff1,xlim = c(minxy,maxxy),
ylim = c(minxy,maxxy),
panel=function(x, y, ...) {
panel.xyplot(x, y, ...);
ltext(x=x, y=y, labels=su$GeneID, pch=c(13,3,16), cex=0.5, lwd=2, pos=1, offset=1, pch = 19)
}
)
}
})
output$plot7<- renderPlot({
req(data())
if( input$datype == 'intensity'){
nchan<- input$chans - 1
}else{
nchan<- input$chans
}
su <- rSu()
reps <- input$reps
index <- channels()
print(.libPaths())
print(all.equal(1:nchan,index))
print(input$reps)
pca <- prcomp(su[,1:length(index)], scale=FALSE)
DTA<-data.frame( as.numeric(t(su[,1:length(index)])%*%pca$x[,1]),
as.numeric(t(su[,1:length(index)])%*%pca$x[,2]))
print(DTA)
p<-ggplot(DTA, aes(x=DTA$as.numeric.t.su...1.length.index........pca.x...1..,
y=DTA$as.numeric.t.su...1.length.index........pca.x...2..))
paste0("PC1", " (", round(pca$sdev[1]/sum(pca$sdev)*100,0), "%)")
shapeval <- c(15:18,7:12)
p <- p + geom_point(aes(colour = factor(rep(1:print(input$reps),each = (nchan)),labels = paste("Rep",1:print(input$reps)))[index],
shape = factor(rep(1:nchan,print(input$reps)),labels = c(paste("C",0:(nchan-1),sep = "")))[index] ), size = 5 ) +
scale_shape_manual(values=shapeval[1:nchan]) + labs(x = paste0("PC1", " (", round(pca$sdev[1]/sum(pca$sdev)*100,0), "%)"),
y = paste0("PC2", " (", round(pca$sdev[2]/sum(pca$sdev)*100,0), "%)"), title="PCA") + labs(color = "Replicates", shape="Concentration")
print(p)
})
output$plot8<- renderPlot({
if( input$modtyp == 'sigmoid'){
plot.new()
title(main = 'Plot not available: Sigmoidal fit applied')
}else{
res<- dataMerge2()
# avgthr=0.2 #sign threshold for the averege fold change 0.3(log2) is 1.3 FC
par(mar=c(5,5,5,10), xpd=TRUE)
# Make a basic volcano plot
with(res, plot(res$AveExpr.x, -log10(res$P.Value), pch=20, main="Volcano plot (slope pval )",
xlab=c("Log2_AvgFC"),ylab=c("-Log10(Pval)"),
xlim=c(-abs(max(res$AveExpr.x)+1),abs(max(res$AveExpr.x)+1))))
# Add colored points: red if padj<0.05, orange of log2FC>1, green if both)
s=subset(res, P.Value< input$pvalsli )
with(s, points(s$AveExpr.x, -log10(s$P.Value), pch=20, col="red"))
s=subset(res, abs(res$AveExpr.x)>input$avthrssli)
with(s, points(s$AveExpr.x, -log10(s$P.Value), pch=20, col="orange"))
s=subset(res, P.Value< input$pvalsli & abs(res$AveExpr.x)>input$avthrssli)
with(s, points(s$AveExpr.x, -log10(s$P.Value), pch=20, col="green"))
# Label points with the textxy function from the calibrate plot
s=subset(res, P.Value< input$pvalsli & abs(res$AveExpr.x)>input$avthrssli)
with(s, textxy( s$AveExpr.x, -log10(s$P.Value), labs=s$GeneID, cex=1)
)
legend("bottomleft", title="Legend",cex = 0.7,
c("Not significant",
paste("P.Value",input$pvalsli, sep = " "), #red
paste("AvgFC >", input$avthrssli, sep=""), #orange,
paste("P.Value", input$pvalsli,"& AvgFC >", input$avthrssli, sep="") #green
),
col=c("black","red","orange","green"),
horiz=FALSE, pch=c(19))
}
})
output$plot9<- renderPlot({
req(data())
if(input$modtyp == 'sigmoid'){
su <- dataMerge()
print(head(su))
if(input$datype =='intensity'){
su1 <- su[,1:(input$chans - 1 )]
}else{
su1 <- su[,1:(input$chans )]
}
} else {
su <- rSu()
vec <- channels()
vec <- length(vec)
su1 <- su[,1:(vec)]
vec.nam <- finalNames()
vec.nam <- vec.nam[channels()]
colnames(su)[match('GeneID.x',colnames(su))] <- 'GeneID'
}
plot.new()
#d3heatmap(su1, Colv = FALSE,labRow = as.character(make.names(su$GeneID,unique = TRUE)), dendrogram = 'row' )
})
output$test<- DT::renderDataTable({
fin<- standardNames()
if(length(input$view_vars) == length(fin)){
DT::datatable(data.frame(Original = input$view_vars,Standard = standardNames(), Final = finalNames()))
}else{
DT::datatable(data.frame(Error = "Incorrect dimensions", Comments= "ensure the number of names selected is the same as the number of channels and repeats inputted"))
}
})
############## Info Boxes
### P value
pvalQc <- reactive({
data.merged <- dataMerge2()
PVal <- c(sum(data.merged$P.Value <= 0.05),sum(data.merged$P.Value.x <= 0.05),
sum(data.merged$P.Value.y <= 0.05))
Names = c("Slope", "Intercept", "Quadratic")
data.frame(Names = Names, PVal = PVal)
})
output$infopvalslo <- renderInfoBox({
temp <- pvalQc()
infoBox(
title = "Slope",paste0(temp[1,2], " p values < 0.05"),color = ifelse(temp[1,2] > 0, "green","orange" ), icon = icon(ifelse(temp[1,2] > 0, "check","warning" ))
)
})
output$infopvalint <- renderInfoBox({
temp <- pvalQc()
infoBox(
title = "Intercept",paste0(temp[2,2], " p values < 0.05"),color = ifelse(temp[2,2] > 0, "green","orange" ), icon = icon(ifelse(temp[2,2] > 0, "check","warning" ))
)
})
output$infopvalquad <- renderInfoBox({
temp <- pvalQc()
infoBox(
title = "Quadratic",paste0(temp[3,2], " p values < 0.05"),color = ifelse(temp[3,2] > 0, "green","orange" ), icon = icon(ifelse(temp[2,2] > 0, "check","warning" ))
)
})
output$corrinfo <- renderInfoBox({
req(data())
if(input$modtyp == 'sigmoid'){
su <- dataMerge()
}else{
su <- rSu()
}
cmat <-cor(su[,channels()],use="pairwise", method = "pearson")
cmat[upper.tri(cmat)]<- 0
cmat<- melt(cmat)
infoBox(
title = NULL,value = ifelse(nrow(cmat[cmat$value < 0, ]) == 0, "No Anti-Correlation between Channels","Anti Correlation between some Channels" ),
color = ifelse(nrow(cmat[cmat$value < 0, ]) == 0, "green","orange" ),
icon = icon(ifelse(nrow(cmat[cmat$value < 0, ]) == 0, "check","warning" ))
)
})
output$siginfodt <- renderInfoBox({
if(input$modtyp == 'lin'){
return(NULL)
} else {
conc<- sigConc()
if(input$datype == 'intensity'){
top<-15 #max prot to plot
data_merged_2 <- dataMerge2()
# RB50<-na.omit(data_merged_2[data_merged_2$RB50Err < as.numeric(summary(data_merged_2$RB50Err)[5]) & data_merged_2$RB50Pval<0.05 & data_merged_2$predX1-data_merged_2$predX9 >0 & data_merged_2$predX1 <= 100,])
RB50 <- data.frame(na.omit(data_merged_2[data_merged_2$RB50Err < as.numeric(summary(data_merged_2$RB50Err)[5]) & data_merged_2$RB50Pval < 0.05
& data_merged_2$predX1-data_merged_2[,paste("predX",(input$chans - 1),sep = "")] >0 & data_merged_2$predX1 <= 100,]))
RB50_ordered<- na.omit(RB50[order(RB50$RB50Pval, decreasing = FALSE),][1:top,])
} else{
pred.names <- sigPredNames()
final.Names <- finalNames()
top<-15 #max prot to plot
data_merged_2 <- dataMerge2()
# RB50<-na.omit(data_merged_2[data_merged_2$RB50Err < as.numeric(summary(data_merged_2$RB50Err)[5]) & data_merged_2$RB50Pval<0.05 & data_merged_2$predX1-data_merged_2$predX9 >0 & data_merged_2$predX1 <= 100,])
RB50 <- data.frame(na.omit(data_merged_2[data_merged_2$RB50Err < as.numeric(summary(data_merged_2$RB50Err)[5]) & data_merged_2$RB50Pval < 0.05
& data_merged_2$predX1-data_merged_2[,paste("predX",input$chans,sep = "")] >0 & data_merged_2$predX1 <= 100,]))
RB50_ordered<- na.omit(RB50[order(RB50$RB50Pval, decreasing = FALSE),][1:top,])
}
infoBox(
title = "RB50",paste0(nrow(RB50_ordered), " Significant RB50"),color = ifelse(nrow(RB50_ordered) > 0, "green","orange" ), icon = icon(ifelse(nrow(RB50_ordered) > 0, "check","warning" ))
)
}
})
output$siginfoslop <- renderInfoBox({
if(input$modtyp == 'lin'){
return(NULL)
} else {
conc<- sigConc()
if(input$datype == 'intensity'){
top<-15 #max prot to plot
conc<- sigConc()
pred.names <- paste0('predX',1:(input$chans -1))
final.Names <- paste0('rep1_C',0:(input$chans - 2))
data_merged_2 <- dataMerge2()
#Here make the subselections for using the ggplot functions SLOPE
slope<-na.omit(data_merged_2[data_merged_2$SlopePval<0.05 ,])
slope_ordered<-na.omit(slope[order(slope$SlopePval, decreasing = FALSE),][1:top,])
} else{
top<-15 #max prot to plot
conc<- sigConc()
pred.names <- sigPredNames()
final.Names <- finalNames()
data_merged_2 <- dataMerge2()
#Here make the subselections for using the ggplot functions SLOPE
slope<-na.omit(data_merged_2[data_merged_2$SlopePval<0.05 ,])
slope_ordered<-na.omit(slope[order(slope$SlopePval, decreasing = FALSE),][1:top,])
}
infoBox(
title = "Slope Coefficient",paste0(nrow(slope_ordered), " Significant Slope"),color = ifelse(nrow(slope_ordered) > 0, "green","orange" ), icon = icon(ifelse(nrow(slope_ordered) > 0, "check","warning" ))
)
}
})
output$siginfodiff <- renderInfoBox({
if(input$modtyp == 'lin'){
return(NULL)
} else {
conc<- sigConc()
if(input$datype == 'intensity'){
data_merged_2 <- dataMerge2()
pred.names <- paste0('predX',1:(input$chans -1))
final.Names <- paste0('rep1_C',0:(input$chans - 2))
topperc<-30 #difference in % between top and bottom
# data_merged_2 <- dataMerge2()
diffinter<- data_merged_2[(data_merged_2$predX1 -data_merged_2[,paste("predX",(input$chans-1),sep = "")]) > topperc & data_merged_2$predX1 <= 100, ]
} else{
conc<- sigConc()
pred.names <- sigPredNames()
final.Names <- finalNames()
topperc<-30 #difference in % between top and bottom
data_merged_2 <- dataMerge2()
diffinter<- data_merged_2[(data_merged_2$predX1 -data_merged_2[,paste("predX",input$chans,sep = "")]) > topperc & data_merged_2$predX1 <= 100, ]
}
infoBox(
title = "Top - Bottom Difference",paste0(nrow(diffinter), " Significant Difference"),color = ifelse(nrow(diffinter) > 0, "green","orange" ), icon = icon(ifelse(nrow(diffinter) > 0, "check","warning" ))
)
}
})
############################
# SIGMOIDAL PLOTS
############################
output$DiffTopBottom <- renderPlot({
if(input$modtyp != 'sigmoid'){
plot.new()
legend('topleft', c("Linear fit applied, no sigmoidal plots available"),bty = 'n')
}else{
if(input$datype == 'intensity'){
data_merged_2 <- dataMerge2()
conc<- sigConc()
pred.names <- paste0('predX',1:(input$chans -1))
final.Names <- paste0('rep1_C',0:(input$chans - 2))
topperc<-30 #difference in % between top and bottom
# data_merged_2 <- dataMerge2()
diffinter<- data_merged_2[(data_merged_2$predX1 -data_merged_2[,paste("predX",(input$chans-1),sep = "")]) > topperc & data_merged_2$predX1 <= 100, ]
if(nrow(diffinter)>0){
Diff_Top_bottom_pred<-shape_for_ggplot_pred(diffinter,log2(conc),pred.names)
Diff_Top_bottom_perc<-shape_for_ggplot_perc(diffinter,log2(conc),final.Names)
what<-c("(Top - Bottom) >")
Diff_Top_bottom<-ggplot()+
geom_line(data = Diff_Top_bottom_pred, aes(x=x,y=value, colour=factor(Diff_Top_bottom_pred$GeneID)), size = 1) +
geom_point(data = Diff_Top_bottom_perc, aes(x=x,y=value, colour=Diff_Top_bottom_perc$GeneID)) +
labs(title=paste(what,topperc,sep=""))
}else{
Diff_Top_bottom<-ggplot()+
labs(title=paste("No significant Top-Bottom >" ,topperc,"%","\n","has been found", sep=""))
}
print(Diff_Top_bottom)
}
else{
conc<- sigConc()
pred.names <- sigPredNames()
final.Names <- finalNames()
topperc<-30 #difference in % between top and bottom
data_merged_2 <- dataMerge2()
diffinter<- data_merged_2[(data_merged_2$predX1 -data_merged_2[,paste("predX",input$chans,sep = "")]) > topperc & data_merged_2$predX1 <= 100, ]
if(nrow(diffinter)>0){
Diff_Top_bottom_pred<-shape_for_ggplot_pred(diffinter,log2(conc),pred.names)
Diff_Top_bottom_perc<-shape_for_ggplot_perc(diffinter,log2(conc),final.Names)
what<-c("(Top - Bottom) >")
Diff_Top_bottom<-ggplot()+
geom_line(data = Diff_Top_bottom_pred, aes(x=x,y=value, colour=factor(Diff_Top_bottom_pred$GeneID)), size = 1) +
geom_point(data = Diff_Top_bottom_perc, aes(x=x,y=value, colour=Diff_Top_bottom_perc$GeneID)) +
labs(title=paste(what,topperc,sep=""))
}else{
Diff_Top_bottom<-ggplot()+
labs(title=paste("No significant Top-Bottom >" ,topperc,"%","\n","has been found", sep=""))
}
print(Diff_Top_bottom)
}
}
})
output$Slope_pl <- renderPlot({
if(input$modtyp != 'sigmoid'){
plot.new()
legend('topleft', c("Linear fit applied, no sigmoidal plots available"),bty = 'n')
}else{
if(input$datype == 'intensity'){
top<-15 #max prot to plot
conc<- sigConc()
pred.names <- paste0('predX',1:(input$chans -1))
final.Names <- paste0('rep1_C',0:(input$chans - 2))
data_merged_2 <- dataMerge2()
#Here make the subselections for using the ggplot functions SLOPE
slope<-na.omit(data_merged_2[data_merged_2$SlopePval<0.05 ,])
slope_ordered<-na.omit(slope[order(slope$SlopePval, decreasing = FALSE),][1:top,])
if(nrow(slope_ordered)>0){
slope_pred<-shape_for_ggplot_pred(slope_ordered,log10(conc),pred.names)
slope_perc<- shape_for_ggplot_perc(slope_ordered,log10(conc),final.Names)
what<-c("Slope (p.val) ")
Slope_pl<-ggplot()+
geom_line(data = slope_pred, aes(x=x,y=value, colour=factor(slope_pred$GeneID)), size = 1) +
geom_point(data = slope_perc, aes(x=x,y=value,colour=slope_perc$GeneID))+
labs(title=paste(what,"Top",top,sep=""))
}else{Slope_pl<-ggplot()+
labs(title="No significant Sigmoidal Slope has been found")
}
print(Slope_pl)
} else{
top<-15 #max prot to plot
conc<- sigConc()
pred.names <- sigPredNames()
final.Names <- finalNames()
data_merged_2 <- dataMerge2()
#Here make the subselections for using the ggplot functions SLOPE
slope<-na.omit(data_merged_2[data_merged_2$SlopePval<0.05 ,])
slope_ordered<-na.omit(slope[order(slope$SlopePval, decreasing = FALSE),][1:top,])
if(nrow(slope_ordered)>0){
slope_pred<-shape_for_ggplot_pred(slope_ordered,log10(conc),pred.names)
slope_perc<- shape_for_ggplot_perc(slope_ordered,log10(conc),final.Names)
what<-c("Slope (p.val) ")
Slope_pl<-ggplot()+
geom_line(data = slope_pred, aes(x=x,y=value, colour=factor(slope_pred$GeneID)), size = 1) +
geom_point(data = slope_perc, aes(x=x,y=value,colour=slope_perc$GeneID))+
labs(title=paste(what,"Top",top,sep=""))
}else{Slope_pl<-ggplot()+
labs(title="No significant Sigmoidal Slope has been found")
}
print(Slope_pl)
}
}
})
output$RB50 <- renderPlot({
if(input$modtyp != 'sigmoid'){
plot.new()
legend('topleft', c("Linear fit applied, no sigmoidal plots available"),bty = 'n')
}else{
if(input$datype =='intensity'){
conc<- sigConc()
pred.names <- paste0('predX',1:(input$chans -1))
final.Names <- paste0('rep1_C',0:(input$chans - 2))
top<-15 #max prot to plot
data_merged_2 <- dataMerge2()
# RB50<-na.omit(data_merged_2[data_merged_2$RB50Err < as.numeric(summary(data_merged_2$RB50Err)[5]) & data_merged_2$RB50Pval<0.05 & data_merged_2$predX1-data_merged_2$predX9 >0 & data_merged_2$predX1 <= 100,])
RB50 <- data.frame(na.omit(data_merged_2[data_merged_2$RB50Err < as.numeric(summary(data_merged_2$RB50Err)[5]) & data_merged_2$RB50Pval < 0.05
& data_merged_2$predX1-data_merged_2[,paste0('predX',(input$chans - 1))] >0 & data_merged_2$predX1 <= 100,]))
RB50_ordered<- na.omit(RB50[order(RB50$RB50Pval, decreasing = FALSE),][1:top,])
if(nrow(RB50_ordered)>0){
RB50_pred<-shape_for_ggplot_pred(RB50_ordered,log10(conc),pred.names)
RB50_perc<-shape_for_ggplot_perc(RB50_ordered,log10(conc),final.Names)
what<-c("RB50 (p.val) ")
RB50_pl<-ggplot()+
geom_line(data = RB50_pred, aes(x=x,y=value, colour=factor(RB50_pred$GeneID)), size = 1) +
geom_point(data = RB50_perc, aes(x=x,y=value,colour=RB50_perc$GeneID))+
labs(title=paste(what,"Top",top,sep=""))
print(RB50_pl)
}else{
RB50_pl<-ggplot()+
labs(title="No significant RB50 has been found")
print(RB50_pl)
}
}else {
conc<- sigConc()
pred.names <- sigPredNames()
final.Names <- finalNames()
top<-15 #max prot to plot
data_merged_2 <- dataMerge2()
# RB50<-na.omit(data_merged_2[data_merged_2$RB50Err < as.numeric(summary(data_merged_2$RB50Err)[5]) & data_merged_2$RB50Pval<0.05 & data_merged_2$predX1-data_merged_2$predX9 >0 & data_merged_2$predX1 <= 100,])
RB50 <- data.frame(na.omit(data_merged_2[data_merged_2$RB50Err < as.numeric(summary(data_merged_2$RB50Err)[5]) & data_merged_2$RB50Pval < 0.05
& data_merged_2$predX1-data_merged_2$predX9 >0 & data_merged_2$predX1 <= 100,]))
RB50_ordered<- na.omit(RB50[order(RB50$RB50Pval, decreasing = FALSE),][1:top,])
if(nrow(RB50_ordered)>0){
RB50_pred<-shape_for_ggplot_pred(RB50_ordered,log10(conc),pred.names)
RB50_perc<-shape_for_ggplot_perc(RB50_ordered,log10(conc),final.Names)
what<-c("RB50 (p.val) ")
RB50_pl<-ggplot()+
geom_line(data = RB50_pred, aes(x=x,y=value, colour=factor(RB50_pred$GeneID)), size = 1) +
geom_point(data = RB50_perc, aes(x=x,y=value,colour=RB50_perc$GeneID))+
labs(title=paste(what,"Top",top,sep=""))
}else{
RB50_pl<-ggplot()+
labs(title="No significant RB50 has been found")
}
print(RB50_pl)
}
}
})
# Linear elements of sigmoidal obselete
# output$Linear_pl1 <- renderPlot({
#
# if(input$modtyp != 'sigmoid'){
# plot.new()
# legend('topleft', c("Linear fit applied, no sigmoidal plots available"),bty = 'n')
# }else{
# conc<- sigConc()
#
# pred.names <- sigPredNames()
# final.Names <- finalNames()
# top<-15 #max prot to plot
#
# data_merged_2 <- dataMerge2()
#
#
# linere<-data_merged_2[data_merged_2$RB50Pval=="lm-fit:intercept.slope.quadratic" & data_merged_2$predX1 > data_merged_2[,paste("predX",input$chans,sep = "")] & data_merged_2$predX1 <= 100 & data_merged_2$Lower_LimitPval < 0.05,]
#
# if(nrow(linere)>0){
# lin_pred<-shape_for_ggplot_pred(linere,log10(conc),pred.names)
# lin_perc<-shape_for_ggplot_perc(linere,log10(conc),final.Names)
# what<-c("Lm model Slope Pval< 0.05 \n (failed dose-resp.) ")
#
# Linear_pl1<-ggplot()+
# geom_line(data = lin_pred, aes(x=x,y=value, colour=factor(lin_pred$GeneID)), size = 1) +
# geom_point(data = lin_perc, aes(x=x,y=value,colour=lin_perc$GeneID))+
# labs(title=paste(what,top,sep=""))
#
#
# }else{
# Linear_pl1<-ggplot()+
# labs(title="No significant Lm slope has been found")
# }
#
# print(Linear_pl1)
# }
# })
#
# output$Linear_pl2 <- renderPlot({
#
# if(input$modtyp != 'sigmoid'){
# plot.new()
# legend('topleft', c("Linear fit applied, no sigmoidal plots available"),bty = 'n')
# }else{
# conc<- sigConc()
# pred.names <- sigPredNames()
# final.Names <- finalNames()
# top<-15 #max prot to plot
#
# data_merged_2 <- dataMerge2()
#
#
# linere<-data_merged_2[data_merged_2$RB50Pval=="lm-fit:intercept.slope.quadratic" & data_merged_2$predX1 > data_merged_2[,paste("predX",input$chans,sep = "")] & data_merged_2$predX1 <= 100 & data_merged_2$Upper_LimitPval < 0.05,]
#
# if(nrow(linere)>0){
# lin_pred<-shape_for_ggplot_pred(linere,log10(conc),pred.names)
# lin_perc<-shape_for_ggplot_perc(linere,log10(conc),final.Names)
# what<-c("Lm model Quadratic Pval< 0.05 \n (failed dose-resp.) ")
#
# Linear_pl2<-ggplot()+
# geom_line(data = lin_pred, aes(x=x,y=value, colour=factor(lin_pred$GeneID)), size = 1) +
# geom_point(data = lin_perc, aes(x=x,y=value,colour=lin_perc$GeneID))+
# labs(title=paste(what,top,sep=""))
#
#
# }else{
# Linear_pl2<-ggplot()+
# labs(title="No significant Lm Quadratic has been found")
# }
#
#
# print(Linear_pl2)
# }
#
# })
#
output$testmerge <- DT::renderDataTable({
# a<- intData()
a<- dataMerge2()
# a <- indexmatrix()
# a <- rSu()
if(input$modtyp == 'sigmoid'){
if(input$incpd == TRUE){
DT::datatable(data.frame(GeneID = a$GeneID, RB50 = a$RB50Coef, RB50pval = a$RB50Pval,Topminusbottom = a$Top_minus_min ,correctedRB50 = a$correctedRB50, depletionConst = a$depletionConstant, Kinase = a$Kinase),
options = list(scrollX = TRUE) )
}else{
DT::datatable(data.frame(GeneID = a$GeneID, RB50 = a$RB50Coef, RB50pval = a$RB50Pval,Topminusbottom = a$Top_minus_min , Kinase = a$Kinase),
options = list(scrollX = TRUE) )
}
} else{
DT::datatable(data.frame(GeneID = a$GeneID.x, Intercept = signif(a$P.Value), Slope = signif(a$P.Value.x), Quadtratic = signif(a$P.Value.y), Kinase = a$Kinase),
options = list(scrollX = TRUE) )
}
})
output$kintab <- DT::renderDataTable({
data.merged <- dataMerge()
proteome<-as.vector(toupper(data.merged$GeneID))
DT::datatable(data.frame(GeneID = intersect(proteome,kinome)))
}
)
#################
## OUTPUT download
#################
output$peprmv<- downloadHandler(
filename = function() {
paste("removedPep", '.csv', sep='')
},
content = function(file) {
write.csv(pepdwn(), file)
}
)
output$report <- downloadHandler(
# For PDF output, change this to "report.pdf"
filename = "report.html",
content = function(file) {
# Copy the report file to a temporary directory before processing it, in
# case we don't have write permissions to the current working dir (which
# can happen when deployed).
tempReport <- file.path(tempdir(), "report.Rmd")
file.copy("report.Rmd", tempReport, overwrite = TRUE)
# Set up parameters to pass to Rmd document
params <- list(chans = input$chans, reps = input$reps, data = dataMerge(), data2 = dataMerge2(), channel = channels(), avthrsli = input$avthrssli,
pvalsli = input$pvalsli, indexmat = indexmatrix(), RSu = rSu(), finNam = finalNames(), datype = input$datype, sigmodin = input$modtyp, concen = sigConc(), sigPred = sigPredNames()
,
vennip = input$venninput, kin = kinome1
# , upVenn <- uploadVenn()
)
# Knit the document, passing in the `params` list, and eval it in a
# child of the global environment (this isolates the code in the document
# from the code in this app).
rmarkdown::render(tempReport, output_file = file,
params = params,
envir = new.env(parent = globalenv())
)
}
)
DownloadData<- reactive({
data.merged <- dataMerge2()
if(input$modtyp != 'sigmoid'){
colnames(data.merged)[match(c('P.Value', 'adj.P.Val', 'P.Value.x', 'adj.P.Val.x', 'P.Value.y', 'adj.P.Val.y'),colnames(data.merged))] <- c( 'P.Value_slope', 'adj.P.Val_slope', 'P.Value_intercept', 'adj.P.Val_intercept','P.Value_quadratic', 'adj.P.Val_quadratic')
}
print(head(data.merged))
data.merged
})
output$downloadData <- downloadHandler(
filename = function() {
paste(input$dataset, '.csv', sep='')
},
content = function(file) {
write.csv(DownloadData(), file)
}
)
## rest elements -- doesn't get rendered
output$testkd<- DT::renderDataTable({
# kd<- rKd()
#
# DT::datatable(data.frame(kd))
# a<- dataMerge2()
# a<- rSu()
# a<- uniprotGene()
a<- DownloadData()
DT::datatable(a,
options = list(scrollX = TRUE) )
})
output$sessionInfo <- renderPrint({
capture.output(sessionInfo())
})
})
# Run the application
shinyApp(ui = ui, server = server)
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