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R/orQAE2.R
In IsoGeneGUI: A graphical user interface to conduct a dose-response analysis of microarray data
Defines functions
`orQAE2`
`orQAE2` <- function(){
# Permutation test for E2
if (!exists("exprs") | !exists("dose")) {
ReturnVal <- tkmessageBox(title="Error Message",message="Load the data first!",icon="error",type="ok")
if (tclvalue(ReturnVal)== "ok") {tkfocus(tt)}
} else {
orqa <- tktoplevel()
tkwm.title(orqa, "Global Likelihood Ratio Test (E2) Analysis: orQA")
spec.frm <- tkframe(orqa, borderwidth=2)
frame1 <- tkframe(spec.frm, relief="groove", borderwidth=2)
buttonFrameasym <-tkframe(orqa, borderwidth=2)
## Select genes and calculate
rb1 <- tkradiobutton(frame1)
rb2 <- tkradiobutton(frame1)
rbValue1 <- tclVar("all")
tkconfigure(rb1, variable=rbValue1, value="all", text="All Genes")
tkconfigure(rb2, variable=rbValue1, value="range", text="Genes Range")
fromgene <- tclVar("")
FromNum <- tkentry(frame1, width="7", textvariable=fromgene)
togene <- tclVar("")
ToNum <- tkentry(frame1, width="7", textvariable=togene)
if (!exists("exprs")) {
valperm <- "1000"
} else {
valperm <- as.character(nrow(exprs)*50)
}
numberPerm <- tclVar(valperm)
numberPermut <- tkentry(frame1, width="7", textvariable=numberPerm)
Calc.orQA <- function (){
if (!exists("exprs")&!exists("dose")) {
ReturnVal <- tkmessageBox(title="Error Message", message="No data set loaded, please load the dataset first!", icon="info", type="ok")
if (tclvalue(ReturnVal)== "ok") {tkfocus(orqa)}
} else {
tkconfigure(orqa, cursor="watch")
rbVal1 <- as.character(tclvalue(rbValue1))
if (rbVal1=="all") {
exprs2orqa <<- exprs
matchID <- c(1:nrow(exprs2orqa))
}
if (rbVal1=="range") {
exprs2orqa <- exprs [tclvalue(fromgene):tclvalue(togene),]
matchID <- c(tclvalue(fromgene):tclvalue(togene))
}
assign("matchIDorqa", matchID, envir=.GlobalEnv)
# foldchange ##
ind <- rep(1, length(dose))
doseCat <- as.numeric(factor(dose,labels=seq(1,length(unique(dose)),by=1)))
res.orQA <<- e2test(data=as.matrix(exprs2orqa), doseCat, B=as.numeric(tclvalue(numberPerm)), rep=ind)
pval.orQA <<- res.orQA$unadj
ProbeID <<- rownames(exprs2orqa)
Mu.Diff <<- MeanDiff(dose, exprs2orqa)
#E2Val.Asymp <<- res.Asymp[,1]
N <- length(ProbeID)
ReturnVal <- tkmessageBox(message="The calculation of the p-values have been finished", icon="info", type="ok")
if (tclvalue(ReturnVal)== "ok") {tkfocus(orqa)}
tkconfigure(orqa, cursor="arrow")
try(tkdelete(treeWidget,"nodeORQA"), silent = TRUE)
try(tkdelete(treeWidget,"orQAPvalNode"), silent = TRUE)
tkinsert(treeWidget, "end", "Record5Node", "orQAPvalNode", text="Raw P-values")
tkinsert(treeWidget, "end", "orQAPvalNode", "NumGeneNodeORQA", text=paste("Number gene analyzed: ",N) )
}
}
Calculate.but <- tkbutton(frame1, text=" Calculate ", command=suppressMessages(Calc.orQA))
lab1 <- tklabel(frame1,text="Calculate the p-values for E2 ")
lab2 <- tklabel(frame1,text="Select the genes: ")
tkgrid.configure(lab1,sticky="w")
tkgrid.configure(lab2,sticky="w")
tkgrid(lab1)
tkgrid(lab2)
tkgrid.configure(rb1, sticky="w")
tkgrid(rb1)
tkgrid(rb2, tklabel(frame1, text="From"), FromNum, tklabel(frame1 ,text="To"), ToNum)
tkgrid.configure(rb2, sticky="w")
tkgrid(tklabel(frame1, text="Number of permutations: "), numberPermut, tklabel(frame1, text=" "), Calculate.but)
tkgrid(frame1)
tkgrid.configure(frame1, sticky="nsw")
## Frame Adjusting the raw p values
frame2 <- tkframe(spec.frm, relief="groove", borderwidth=2)
cb1 <- tkcheckbutton(frame2)
cb2 <- tkcheckbutton(frame2)
cb3 <- tkcheckbutton(frame2)
cb4 <- tkcheckbutton(frame2)
cb5 <- tkcheckbutton(frame2)
cb6 <- tkcheckbutton(frame2)
cb7 <- tkcheckbutton(frame2)
cbValue1 <- tclVar("1")
cbValue2 <- tclVar("0")
cbValue3 <- tclVar("0")
cbValue4 <- tclVar("0")
cbValue5 <- tclVar("0")
cbValue6 <- tclVar("0")
cbValue7 <- tclVar("0")
tkconfigure(cb1, variable=cbValue1, text="BH")
tkconfigure(cb2, variable=cbValue2, text="BY")
tkconfigure(cb3, variable=cbValue3, text="SidakSS")
tkconfigure(cb4, variable=cbValue4, text="SidakSD")
tkconfigure(cb5, variable=cbValue5, text="Holm")
tkconfigure(cb6, variable=cbValue6, text="Hochberg")
tkconfigure(cb7, variable=cbValue7, text="Bonferroni")
label.pvalAdj <- tklabel(frame2, text="P-value adjustment: ")
tkgrid(label.pvalAdj)
tkgrid.configure(label.pvalAdj, sticky="w")
tkgrid(cb1, cb2, cb3, cb4)
tkgrid(cb5, cb6, cb7)
tkgrid.configure(cb1, cb2, cb3, cb4, cb5, cb6, cb7, sticky="w")
FDR <- tclVar("0.05")
FDRtxt <- tkentry(frame2, width="5", textvariable=FDR)
tkgrid(tklabel(frame2, text="Overall Significant Level: "), FDRtxt)
cb10 <- tkcheckbutton(frame2)
cbValue10 <- tclVar("0")
tkconfigure(cb10, variable=cbValue10, text="Display the significant genes")
tkgrid(cb10)
AdjustBut <- function(){
if (!exists("pval.orQA")) {
ReturnVal <- tkmessageBox(title="Error Message", message="The raw-pvalues have been not calculated yet!",
icon="info", type="ok")
if (tclvalue(ReturnVal) == "ok") {tkfocus(orqa)}
} else {
tkconfigure(orqa,cursor="watch")
cbVal1 <- as.character(tclvalue(cbValue1))
cbVal2 <- as.character(tclvalue(cbValue2))
cbVal3 <- as.character(tclvalue(cbValue3))
cbVal4 <- as.character(tclvalue(cbValue4))
cbVal5 <- as.character(tclvalue(cbValue5))
cbVal6 <- as.character(tclvalue(cbValue6))
cbVal7 <- as.character(tclvalue(cbValue7))
cbVal10 <- as.character(tclvalue(cbValue10))
E2Val <- pval.orQA
FDRval <<- as.numeric(tclvalue(FDR))
Direction <- res.orQA$dir
Direction[Direction==TRUE] <- "up"
Direction[Direction==FALSE] <- "dn"
try(tkdelete(treeWidget,"AdjPvalORQANode"), silent = TRUE)
tkinsert(treeWidget,"end","Record5Node", "AdjPvalORQANode", text= paste("Adjusted P-values, FDR: ", FDRval))
sigeneBHorqa <<- sigeneBYorqa <<- sigeneSSorqa <<- sigeneSDorqa <<- sigeneHolmorqa <<- sigeneHochorqa <<- sigeneBonorqa <<- NULL
adjpBHorqa <<- adjpBYorqa <<- adjpSSorqa <<- adjpSDorqa <<- adjpHolmorqa <<- adjpHochorqa <<- adjpBonorqa <<- NULL
result <- matrix(NA,7,4)
numsigBH <- numsigBY <- numsigSS <- numsigSD <- numsigHolm <- numsigHoch <- numsigBon <- 0
if (cbVal1=="1") {
adjpBHorqa <- adjustment(pval.orQA,"BH")
assign("adjpBHorqa", adjpBHorqa ,envir=.GlobalEnv)
sigeneBHorqa <- Signif(pval.orQA, FDRval, "BH")
numsigBH <- nrow(sigeneBHorqa)
numsigBH [is.null(numsigBH)] <- 0
result[1, ] <- c("BH", numsigBH, 1, 1)
tkinsert(treeWidget, "end", "AdjPvalORQANode","BHNodeORQA", text= paste("BH, Sig:", numsigBH))
}
if (cbVal2=="1") {
adjpBYorqa <- adjustment(pval.orQA, "BY")
assign("adjpBYorqa", adjpBYorqa, envir=.GlobalEnv)
sigeneBYorqa <- Signif(pval.orQA, FDRval, "BY")
numsigBY <- nrow(sigeneBYorqa)
numsigBY[is.null(numsigBY)] <- 0
result[2,] <- c("BY", numsigBY, 3, 1)
tkinsert(treeWidget, "end", "AdjPvalORQANode", "BYNodeORQA", text= paste("BY, Sig:", numsigBY))
}
if (cbVal3=="1") {
adjpSSorqa <- adjustment(pval.orQA, "SidakSS")
assign("adjpSSorqa", adjpSSorqa, envir=.GlobalEnv)
sigeneSSorqa <- Signif(pval.orQA, FDRval, "SidakSS")
numsigSS <- nrow(sigeneSSorqa)
numsigSS [is.null(numsigSS)] <- 0
result[3,] <- c("SidakSS", numsigSS, 4, 1)
tkinsert(treeWidget, "end", "AdjPvalORQANode", "Sidak1NodeORQA", text= paste ("Sidak SS, Sig:", numsigSS))
}
if (cbVal4=="1") {
adjpSDorqa <- adjustment(pval.orQA,"SidakSD")
assign("adjpSDorqa", adjpSDorqa, envir=.GlobalEnv)
sigeneSDorqa <- Signif(pval.orQA, FDRval, "SidakSD")
numsigSD <- nrow(sigeneSDorqa)
numsigSD [is.null(numsigSD)] <- 0
result[4, ] <- c("SidakSD", numsigSD, 1, 2)
tkinsert(treeWidget, "end", "AdjPvalORQANode", "Sidak2NodeORQA", text= paste ("Sidak SD, Sig:", numsigSD))
}
if (cbVal5=="1") {
adjpHolmorqa <- adjustment(pval.orQA, "Holm")
assign("adjpHolmorqa", adjpHolmorqa, envir=.GlobalEnv)
sigeneHolmorqa <- Signif(pval.orQA, FDRval, "Holm")
numsigHolm <- nrow(sigeneHolmorqa )
numsigHolm[is.null(numsigHolm )] <- 0
result[5,] <- c("Holm", numsigHolm, 2, 2)
tkinsert(treeWidget, "end", "AdjPvalORQANode", "HolmNodeORQA", text= paste( "Holm, Sig:", numsigHolm))
}
if (cbVal6=="1") {
adjpHochorqa <- adjustment(pval.orQA, "Hochberg")
assign("adjpHochorqa", adjpHochorqa, envir=.GlobalEnv)
sigeneHochorqa <- Signif(pval.orQA, FDRval, "Hochberg")
numsigHoch <- nrow(sigeneHochorqa)
numsigHoch[is.null(numsigHoch)] <- 0
result[6, ] <- c("Hochberg", numsigHoch, 3, 2)
tkinsert(treeWidget, "end", "AdjPvalORQANode", "HocbergNodeORQA", text= paste ("Hocberg, Sig:", numsigHoch))
}
if (cbVal7=="1") {
adjpBonorqa <- adjustment(pval.orQA, "Bonferroni")
assign("adjpBonorqa", adjpBonorqa, envir=.GlobalEnv)
sigeneBonorqa <- Signif(pval.orQA, FDRval, "Bonferroni")
numsigBon <- nrow(sigeneBonorqa)
numsigBon[is.null(numsigBon)] <- 0
result[7, ] <- c("Bonferroni", numsigBon, 4, 2)
tkinsert(treeWidget, "end", "AdjPvalORQANode", "BonferroniNodeORQA", text=paste("Bonferroni, Sig:", numsigBon))
}
num <- nrow(exprs2orqa)
result2 <- na.exclude(result)
colnames(result2) <- c("P-values Adjustment", "Number of significant genes", "color", "line type")
if (nrow(result2) > 1){
try(showData(result2[, 1:2], title= paste("Number of Significant Genes, FDR:", FDRval ," Number of Genes analyzed:", num)))
}
if (nrow(result2) == 1) {printOrQA(num, FDRval, result2)}
RowNumSig <- NULL
if (numsigBH > 0) {RowNumSig <- unique(c(RowNumSig,sigeneBHorqa$row.num))}
if (numsigBY > 0) {RowNumSig <- unique(c(RowNumSig,sigeneBYorqa$row.num))}
if (numsigSS > 0) {RowNumSig <- unique(c(RowNumSig,sigeneSSorqa$row.num))}
if (numsigSD > 0) {RowNumSig <- unique(c(RowNumSig,sigeneSDorqa$row.num))}
if (numsigHolm > 0) {RowNumSig <- unique(c(RowNumSig,sigeneHolmorqa$row.num))}
if (numsigHoch > 0) {RowNumSig <- unique(c(RowNumSig,sigeneHochorqa$row.num))}
if (numsigBon > 0) {RowNumSig <- unique(c(RowNumSig,sigeneBonorqa$row.num))}
#RowNumSig <- unique(c(sigeneBHorqa$row.num, sigeneBYorqa$row.num, sigeneSSorqa$row.num, sigeneSDorqa$row.num,
# sigeneHolmorqa$row.num, sigeneHochorqa$row.num, sigeneBonorqa$row.num))
AdjPvalAll <- cbind(adjpBHorqa[,2], adjpBYorqa[,2], adjpSSorqa[,2], adjpSDorqa[,2],
adjpHolmorqa[,2], adjpHochorqa[,2], adjpBonorqa[,2])
colnames(AdjPvalAll) <- paste(result2[, 1], "p-val")
if (ncol(AdjPvalAll) == 1) {
PvalSig <- AdjPvalAll[RowNumSig,]
orderedRowNum <- RowNumSig[order(PvalSig)]
} else {
sumSig <- apply(AdjPvalAll[RowNumSig,], 1, sum)
orderedRowNum <- RowNumSig[order(sumSig)]
}
AdjPvalAll <- round(AdjPvalAll, digits = 6)
row.num <- 1:nrow(exprs2orqa)
Res.orQA <<- data.frame(ProbeID, row.num, Mu.Diff, Direction, pval.orQA, AdjPvalAll)
rownames(Res.orQA) <<- NULL
orQASigGenes1 <- Res.orQA[orderedRowNum,]
rownames(orQASigGenes1) <- NULL
SigGenes.orqaE2 <<- orQASigGenes1
if(cbVal10=="1" ) {
try(showData(orQASigGenes1, title= paste("List of Significant Genes based on permutations p-values (orQA), FDR:",
FDRval, " Number of Genes analyzed :", num)))
}
tkconfigure(orqa, cursor="arrow")
result3 <<- result2
assign("result3orqa", result3, envir=.GlobalEnv)
}
}
run.but <- tkbutton(frame2, text=" Calculate ", command = AdjustBut)
tkgrid(tklabel(frame2,text=" "), run.but)
tkgrid(tklabel(frame2,text=" "))
savesiggene <- function() {
save.result(SigGenes.orqaE2)
}
savesiggene.but <- tkbutton(frame2, text="Save significant genes", command=savesiggene)
saveallgene <- function() {
Pval.AllGenes.orQA <<- Res.orQA
save.result(Pval.AllGenes.orQA)
}
saveallgene.but <- tkbutton(frame2, text="Save results for all genes", command=saveallgene)
tkgrid.configure(savesiggene.but, saveallgene.but, sticky="w")
tkgrid(frame2)
tkgrid.configure(frame2, sticky="w")
#### Frame for Producing Plots ##
frame3 <- tkframe(spec.frm, relief="groove", borderwidth=2)
cb9 <- tkcheckbutton(frame3)
cb11 <- tkcheckbutton(frame3)
cbValue9 <- tclVar("0")
cbValue11 <- tclVar("0")
tkconfigure(cb9,variable=cbValue9,text="Ranking Plot (Adjust the p-values first)")
tkconfigure(cb11,variable=cbValue11,text="Plot Fold change vs p-values")
label.plots <-tklabel(frame3,text="Plots: ")
tkgrid(label.plots)
tkgrid.configure(label.plots,sticky="w")
tkgrid.configure(cb11,sticky="w")
tkgrid.configure(cb9,sticky="w")
tkgrid(cb11)
tkgrid(cb9)
PlotBut <- function () {
if (!exists("pval.orQA")){
ReturnVal <- tkmessageBox(title="Error Message",message="The raw-pvalues have not calculated yet!",icon="info",type="ok")
if (tclvalue(ReturnVal)== "ok") {tkfocus(orqa)}
}
else {
tkconfigure(orqa, cursor="watch")
cbVal9 <- as.character(tclvalue(cbValue9))
cbVal11 <- as.character(tclvalue(cbValue11))
if (cbVal9=="1" ){
tkconfigure(orqa, cursor="watch")
rankPlot <- function() {
if (!exists("result3")) {
params <- par(bg="white")
options(show.error.messages = FALSE)
plot((1:nrow(exprs2orqa)), main="P-values", xlab=" Index ", ylab="Raw P-values", ylim=c(0,1))
try(lines(sort(pval.orQA), col=2, lwd=2, lty=1, type="s"))
} else {
params <- par(bg="white")
options(warn = -1)
plot((1:nrow(exprs2orqa)), main="P-values", xlab=" Index ", ylab="P-values", ylim=c(0,1))
try(lines(sort(adjpBHorqa[, 2]), col=1, lwd=2, lty=1, type="s"), TRUE)
try(lines(sort(adjpBYorqa[, 2]), col=3, lwd=2, lty=1, type="s"), TRUE)
try(lines(sort(adjpSSorqa[, 2]), col=4, lwd=2, lty=1, type="s"), TRUE)
try(lines(sort(adjpSDorqa[, 2]), col=1, lwd=2, lty=1, type="s"), TRUE)
try(lines(sort(adjpHolmorqa[, 2]), col=2,lwd=2, lty=2, type="s"), TRUE)
try(lines(sort(adjpHochorqa[, 2]), col=3,lwd=2, lty=2, type="s"), TRUE)
try(lines(sort(adjpBonorqa[, 2]), col=4, lwd=2, lty=2, type="s"), TRUE)
try(lines(sort(pval.orQA), col=2, lwd=2, lty=1, type="s"))
abline(FDRval, 0)
metd <- result3[, 1]
col <- result3[, 3]
type <- result3[, 4]
legend((0.7*nrow(exprs2orqa)), 0.62, c("Raw P-val",metd),
col = c(2, as.numeric(col)), lty = c(1, as.numeric(type)), lwd = 2, merge = TRUE )
options(warn = 1)
}
}
Plot2(rankPlot, 1.7, 1.5, title="Windows Graph Output: Plot p-values")
}
if (cbVal11=="1") {
PVALSvsDiffPlot <- function () {
params <- par(bg="white")
options(show.error.messages = FALSE)
x <- cbind(Mu.Diff, -log(pval.orQA))
colors <- densCols(x)
plot (x,col=colors, pch=20, lwd=3,ylab="- log p-values", xlab="Fold change" )
}
Plot2(PVALSvsDiffPlot, 1.5, 1.5, title="Windows Graph Output: Fold change vs p-values" )
## Fold change = > Mu*dose.max-Mu*dose.min ##
}
tkconfigure(orqa, cursor="arrow")
options(show.error.messages = TRUE)
}
}
plot.but <-tkbutton(frame3,text=" Produce plots ", command=PlotBut)
tkgrid(tklabel(frame3,text=" "), plot.but)
tkgrid(frame3)
tkgrid.configure(frame3,sticky="nsw")
onExit <- function(){
ReturnVal <<- 0
tkdestroy(orqa)
}
tkgrid(tklabel(buttonFrameasym, text=" "))
Exit.but <- tkbutton(buttonFrameasym, text=" Exit the analysis ", command=onExit )
tkgrid(Exit.but)
tkgrid.configure(Exit.but, sticky="e")
tkgrid(spec.frm)
tkgrid(buttonFrameasym)
}
}
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IsoGeneGUI documentation built on Nov. 8, 2020, 5:52 p.m.
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Defines functions `orQAE2`
`orQAE2` <- function(){
# Permutation test for E2
if (!exists("exprs") | !exists("dose")) {
ReturnVal <- tkmessageBox(title="Error Message",message="Load the data first!",icon="error",type="ok")
if (tclvalue(ReturnVal)== "ok") {tkfocus(tt)}
} else {
orqa <- tktoplevel()
tkwm.title(orqa, "Global Likelihood Ratio Test (E2) Analysis: orQA")
spec.frm <- tkframe(orqa, borderwidth=2)
frame1 <- tkframe(spec.frm, relief="groove", borderwidth=2)
buttonFrameasym <-tkframe(orqa, borderwidth=2)
## Select genes and calculate
rb1 <- tkradiobutton(frame1)
rb2 <- tkradiobutton(frame1)
rbValue1 <- tclVar("all")
tkconfigure(rb1, variable=rbValue1, value="all", text="All Genes")
tkconfigure(rb2, variable=rbValue1, value="range", text="Genes Range")
fromgene <- tclVar("")
FromNum <- tkentry(frame1, width="7", textvariable=fromgene)
togene <- tclVar("")
ToNum <- tkentry(frame1, width="7", textvariable=togene)
if (!exists("exprs")) {
valperm <- "1000"
} else {
valperm <- as.character(nrow(exprs)*50)
}
numberPerm <- tclVar(valperm)
numberPermut <- tkentry(frame1, width="7", textvariable=numberPerm)
Calc.orQA <- function (){
if (!exists("exprs")&!exists("dose")) {
ReturnVal <- tkmessageBox(title="Error Message", message="No data set loaded, please load the dataset first!", icon="info", type="ok")
if (tclvalue(ReturnVal)== "ok") {tkfocus(orqa)}
} else {
tkconfigure(orqa, cursor="watch")
rbVal1 <- as.character(tclvalue(rbValue1))
if (rbVal1=="all") {
exprs2orqa <<- exprs
matchID <- c(1:nrow(exprs2orqa))
}
if (rbVal1=="range") {
exprs2orqa <- exprs [tclvalue(fromgene):tclvalue(togene),]
matchID <- c(tclvalue(fromgene):tclvalue(togene))
}
assign("matchIDorqa", matchID, envir=.GlobalEnv)
# foldchange ##
ind <- rep(1, length(dose))
doseCat <- as.numeric(factor(dose,labels=seq(1,length(unique(dose)),by=1)))
res.orQA <<- e2test(data=as.matrix(exprs2orqa), doseCat, B=as.numeric(tclvalue(numberPerm)), rep=ind)
pval.orQA <<- res.orQA$unadj
ProbeID <<- rownames(exprs2orqa)
Mu.Diff <<- MeanDiff(dose, exprs2orqa)
#E2Val.Asymp <<- res.Asymp[,1]
N <- length(ProbeID)
ReturnVal <- tkmessageBox(message="The calculation of the p-values have been finished", icon="info", type="ok")
if (tclvalue(ReturnVal)== "ok") {tkfocus(orqa)}
tkconfigure(orqa, cursor="arrow")
try(tkdelete(treeWidget,"nodeORQA"), silent = TRUE)
try(tkdelete(treeWidget,"orQAPvalNode"), silent = TRUE)
tkinsert(treeWidget, "end", "Record5Node", "orQAPvalNode", text="Raw P-values")
tkinsert(treeWidget, "end", "orQAPvalNode", "NumGeneNodeORQA", text=paste("Number gene analyzed: ",N) )
}
}
Calculate.but <- tkbutton(frame1, text=" Calculate ", command=suppressMessages(Calc.orQA))
lab1 <- tklabel(frame1,text="Calculate the p-values for E2 ")
lab2 <- tklabel(frame1,text="Select the genes: ")
tkgrid.configure(lab1,sticky="w")
tkgrid.configure(lab2,sticky="w")
tkgrid(lab1)
tkgrid(lab2)
tkgrid.configure(rb1, sticky="w")
tkgrid(rb1)
tkgrid(rb2, tklabel(frame1, text="From"), FromNum, tklabel(frame1 ,text="To"), ToNum)
tkgrid.configure(rb2, sticky="w")
tkgrid(tklabel(frame1, text="Number of permutations: "), numberPermut, tklabel(frame1, text=" "), Calculate.but)
tkgrid(frame1)
tkgrid.configure(frame1, sticky="nsw")
## Frame Adjusting the raw p values
frame2 <- tkframe(spec.frm, relief="groove", borderwidth=2)
cb1 <- tkcheckbutton(frame2)
cb2 <- tkcheckbutton(frame2)
cb3 <- tkcheckbutton(frame2)
cb4 <- tkcheckbutton(frame2)
cb5 <- tkcheckbutton(frame2)
cb6 <- tkcheckbutton(frame2)
cb7 <- tkcheckbutton(frame2)
cbValue1 <- tclVar("1")
cbValue2 <- tclVar("0")
cbValue3 <- tclVar("0")
cbValue4 <- tclVar("0")
cbValue5 <- tclVar("0")
cbValue6 <- tclVar("0")
cbValue7 <- tclVar("0")
tkconfigure(cb1, variable=cbValue1, text="BH")
tkconfigure(cb2, variable=cbValue2, text="BY")
tkconfigure(cb3, variable=cbValue3, text="SidakSS")
tkconfigure(cb4, variable=cbValue4, text="SidakSD")
tkconfigure(cb5, variable=cbValue5, text="Holm")
tkconfigure(cb6, variable=cbValue6, text="Hochberg")
tkconfigure(cb7, variable=cbValue7, text="Bonferroni")
label.pvalAdj <- tklabel(frame2, text="P-value adjustment: ")
tkgrid(label.pvalAdj)
tkgrid.configure(label.pvalAdj, sticky="w")
tkgrid(cb1, cb2, cb3, cb4)
tkgrid(cb5, cb6, cb7)
tkgrid.configure(cb1, cb2, cb3, cb4, cb5, cb6, cb7, sticky="w")
FDR <- tclVar("0.05")
FDRtxt <- tkentry(frame2, width="5", textvariable=FDR)
tkgrid(tklabel(frame2, text="Overall Significant Level: "), FDRtxt)
cb10 <- tkcheckbutton(frame2)
cbValue10 <- tclVar("0")
tkconfigure(cb10, variable=cbValue10, text="Display the significant genes")
tkgrid(cb10)
AdjustBut <- function(){
if (!exists("pval.orQA")) {
ReturnVal <- tkmessageBox(title="Error Message", message="The raw-pvalues have been not calculated yet!",
icon="info", type="ok")
if (tclvalue(ReturnVal) == "ok") {tkfocus(orqa)}
} else {
tkconfigure(orqa,cursor="watch")
cbVal1 <- as.character(tclvalue(cbValue1))
cbVal2 <- as.character(tclvalue(cbValue2))
cbVal3 <- as.character(tclvalue(cbValue3))
cbVal4 <- as.character(tclvalue(cbValue4))
cbVal5 <- as.character(tclvalue(cbValue5))
cbVal6 <- as.character(tclvalue(cbValue6))
cbVal7 <- as.character(tclvalue(cbValue7))
cbVal10 <- as.character(tclvalue(cbValue10))
E2Val <- pval.orQA
FDRval <<- as.numeric(tclvalue(FDR))
Direction <- res.orQA$dir
Direction[Direction==TRUE] <- "up"
Direction[Direction==FALSE] <- "dn"
try(tkdelete(treeWidget,"AdjPvalORQANode"), silent = TRUE)
tkinsert(treeWidget,"end","Record5Node", "AdjPvalORQANode", text= paste("Adjusted P-values, FDR: ", FDRval))
sigeneBHorqa <<- sigeneBYorqa <<- sigeneSSorqa <<- sigeneSDorqa <<- sigeneHolmorqa <<- sigeneHochorqa <<- sigeneBonorqa <<- NULL
adjpBHorqa <<- adjpBYorqa <<- adjpSSorqa <<- adjpSDorqa <<- adjpHolmorqa <<- adjpHochorqa <<- adjpBonorqa <<- NULL
result <- matrix(NA,7,4)
numsigBH <- numsigBY <- numsigSS <- numsigSD <- numsigHolm <- numsigHoch <- numsigBon <- 0
if (cbVal1=="1") {
adjpBHorqa <- adjustment(pval.orQA,"BH")
assign("adjpBHorqa", adjpBHorqa ,envir=.GlobalEnv)
sigeneBHorqa <- Signif(pval.orQA, FDRval, "BH")
numsigBH <- nrow(sigeneBHorqa)
numsigBH [is.null(numsigBH)] <- 0
result[1, ] <- c("BH", numsigBH, 1, 1)
tkinsert(treeWidget, "end", "AdjPvalORQANode","BHNodeORQA", text= paste("BH, Sig:", numsigBH))
}
if (cbVal2=="1") {
adjpBYorqa <- adjustment(pval.orQA, "BY")
assign("adjpBYorqa", adjpBYorqa, envir=.GlobalEnv)
sigeneBYorqa <- Signif(pval.orQA, FDRval, "BY")
numsigBY <- nrow(sigeneBYorqa)
numsigBY[is.null(numsigBY)] <- 0
result[2,] <- c("BY", numsigBY, 3, 1)
tkinsert(treeWidget, "end", "AdjPvalORQANode", "BYNodeORQA", text= paste("BY, Sig:", numsigBY))
}
if (cbVal3=="1") {
adjpSSorqa <- adjustment(pval.orQA, "SidakSS")
assign("adjpSSorqa", adjpSSorqa, envir=.GlobalEnv)
sigeneSSorqa <- Signif(pval.orQA, FDRval, "SidakSS")
numsigSS <- nrow(sigeneSSorqa)
numsigSS [is.null(numsigSS)] <- 0
result[3,] <- c("SidakSS", numsigSS, 4, 1)
tkinsert(treeWidget, "end", "AdjPvalORQANode", "Sidak1NodeORQA", text= paste ("Sidak SS, Sig:", numsigSS))
}
if (cbVal4=="1") {
adjpSDorqa <- adjustment(pval.orQA,"SidakSD")
assign("adjpSDorqa", adjpSDorqa, envir=.GlobalEnv)
sigeneSDorqa <- Signif(pval.orQA, FDRval, "SidakSD")
numsigSD <- nrow(sigeneSDorqa)
numsigSD [is.null(numsigSD)] <- 0
result[4, ] <- c("SidakSD", numsigSD, 1, 2)
tkinsert(treeWidget, "end", "AdjPvalORQANode", "Sidak2NodeORQA", text= paste ("Sidak SD, Sig:", numsigSD))
}
if (cbVal5=="1") {
adjpHolmorqa <- adjustment(pval.orQA, "Holm")
assign("adjpHolmorqa", adjpHolmorqa, envir=.GlobalEnv)
sigeneHolmorqa <- Signif(pval.orQA, FDRval, "Holm")
numsigHolm <- nrow(sigeneHolmorqa )
numsigHolm[is.null(numsigHolm )] <- 0
result[5,] <- c("Holm", numsigHolm, 2, 2)
tkinsert(treeWidget, "end", "AdjPvalORQANode", "HolmNodeORQA", text= paste( "Holm, Sig:", numsigHolm))
}
if (cbVal6=="1") {
adjpHochorqa <- adjustment(pval.orQA, "Hochberg")
assign("adjpHochorqa", adjpHochorqa, envir=.GlobalEnv)
sigeneHochorqa <- Signif(pval.orQA, FDRval, "Hochberg")
numsigHoch <- nrow(sigeneHochorqa)
numsigHoch[is.null(numsigHoch)] <- 0
result[6, ] <- c("Hochberg", numsigHoch, 3, 2)
tkinsert(treeWidget, "end", "AdjPvalORQANode", "HocbergNodeORQA", text= paste ("Hocberg, Sig:", numsigHoch))
}
if (cbVal7=="1") {
adjpBonorqa <- adjustment(pval.orQA, "Bonferroni")
assign("adjpBonorqa", adjpBonorqa, envir=.GlobalEnv)
sigeneBonorqa <- Signif(pval.orQA, FDRval, "Bonferroni")
numsigBon <- nrow(sigeneBonorqa)
numsigBon[is.null(numsigBon)] <- 0
result[7, ] <- c("Bonferroni", numsigBon, 4, 2)
tkinsert(treeWidget, "end", "AdjPvalORQANode", "BonferroniNodeORQA", text=paste("Bonferroni, Sig:", numsigBon))
}
num <- nrow(exprs2orqa)
result2 <- na.exclude(result)
colnames(result2) <- c("P-values Adjustment", "Number of significant genes", "color", "line type")
if (nrow(result2) > 1){
try(showData(result2[, 1:2], title= paste("Number of Significant Genes, FDR:", FDRval ," Number of Genes analyzed:", num)))
}
if (nrow(result2) == 1) {printOrQA(num, FDRval, result2)}
RowNumSig <- NULL
if (numsigBH > 0) {RowNumSig <- unique(c(RowNumSig,sigeneBHorqa$row.num))}
if (numsigBY > 0) {RowNumSig <- unique(c(RowNumSig,sigeneBYorqa$row.num))}
if (numsigSS > 0) {RowNumSig <- unique(c(RowNumSig,sigeneSSorqa$row.num))}
if (numsigSD > 0) {RowNumSig <- unique(c(RowNumSig,sigeneSDorqa$row.num))}
if (numsigHolm > 0) {RowNumSig <- unique(c(RowNumSig,sigeneHolmorqa$row.num))}
if (numsigHoch > 0) {RowNumSig <- unique(c(RowNumSig,sigeneHochorqa$row.num))}
if (numsigBon > 0) {RowNumSig <- unique(c(RowNumSig,sigeneBonorqa$row.num))}
#RowNumSig <- unique(c(sigeneBHorqa$row.num, sigeneBYorqa$row.num, sigeneSSorqa$row.num, sigeneSDorqa$row.num,
# sigeneHolmorqa$row.num, sigeneHochorqa$row.num, sigeneBonorqa$row.num))
AdjPvalAll <- cbind(adjpBHorqa[,2], adjpBYorqa[,2], adjpSSorqa[,2], adjpSDorqa[,2],
adjpHolmorqa[,2], adjpHochorqa[,2], adjpBonorqa[,2])
colnames(AdjPvalAll) <- paste(result2[, 1], "p-val")
if (ncol(AdjPvalAll) == 1) {
PvalSig <- AdjPvalAll[RowNumSig,]
orderedRowNum <- RowNumSig[order(PvalSig)]
} else {
sumSig <- apply(AdjPvalAll[RowNumSig,], 1, sum)
orderedRowNum <- RowNumSig[order(sumSig)]
}
AdjPvalAll <- round(AdjPvalAll, digits = 6)
row.num <- 1:nrow(exprs2orqa)
Res.orQA <<- data.frame(ProbeID, row.num, Mu.Diff, Direction, pval.orQA, AdjPvalAll)
rownames(Res.orQA) <<- NULL
orQASigGenes1 <- Res.orQA[orderedRowNum,]
rownames(orQASigGenes1) <- NULL
SigGenes.orqaE2 <<- orQASigGenes1
if(cbVal10=="1" ) {
try(showData(orQASigGenes1, title= paste("List of Significant Genes based on permutations p-values (orQA), FDR:",
FDRval, " Number of Genes analyzed :", num)))
}
tkconfigure(orqa, cursor="arrow")
result3 <<- result2
assign("result3orqa", result3, envir=.GlobalEnv)
}
}
run.but <- tkbutton(frame2, text=" Calculate ", command = AdjustBut)
tkgrid(tklabel(frame2,text=" "), run.but)
tkgrid(tklabel(frame2,text=" "))
savesiggene <- function() {
save.result(SigGenes.orqaE2)
}
savesiggene.but <- tkbutton(frame2, text="Save significant genes", command=savesiggene)
saveallgene <- function() {
Pval.AllGenes.orQA <<- Res.orQA
save.result(Pval.AllGenes.orQA)
}
saveallgene.but <- tkbutton(frame2, text="Save results for all genes", command=saveallgene)
tkgrid.configure(savesiggene.but, saveallgene.but, sticky="w")
tkgrid(frame2)
tkgrid.configure(frame2, sticky="w")
#### Frame for Producing Plots ##
frame3 <- tkframe(spec.frm, relief="groove", borderwidth=2)
cb9 <- tkcheckbutton(frame3)
cb11 <- tkcheckbutton(frame3)
cbValue9 <- tclVar("0")
cbValue11 <- tclVar("0")
tkconfigure(cb9,variable=cbValue9,text="Ranking Plot (Adjust the p-values first)")
tkconfigure(cb11,variable=cbValue11,text="Plot Fold change vs p-values")
label.plots <-tklabel(frame3,text="Plots: ")
tkgrid(label.plots)
tkgrid.configure(label.plots,sticky="w")
tkgrid.configure(cb11,sticky="w")
tkgrid.configure(cb9,sticky="w")
tkgrid(cb11)
tkgrid(cb9)
PlotBut <- function () {
if (!exists("pval.orQA")){
ReturnVal <- tkmessageBox(title="Error Message",message="The raw-pvalues have not calculated yet!",icon="info",type="ok")
if (tclvalue(ReturnVal)== "ok") {tkfocus(orqa)}
}
else {
tkconfigure(orqa, cursor="watch")
cbVal9 <- as.character(tclvalue(cbValue9))
cbVal11 <- as.character(tclvalue(cbValue11))
if (cbVal9=="1" ){
tkconfigure(orqa, cursor="watch")
rankPlot <- function() {
if (!exists("result3")) {
params <- par(bg="white")
options(show.error.messages = FALSE)
plot((1:nrow(exprs2orqa)), main="P-values", xlab=" Index ", ylab="Raw P-values", ylim=c(0,1))
try(lines(sort(pval.orQA), col=2, lwd=2, lty=1, type="s"))
} else {
params <- par(bg="white")
options(warn = -1)
plot((1:nrow(exprs2orqa)), main="P-values", xlab=" Index ", ylab="P-values", ylim=c(0,1))
try(lines(sort(adjpBHorqa[, 2]), col=1, lwd=2, lty=1, type="s"), TRUE)
try(lines(sort(adjpBYorqa[, 2]), col=3, lwd=2, lty=1, type="s"), TRUE)
try(lines(sort(adjpSSorqa[, 2]), col=4, lwd=2, lty=1, type="s"), TRUE)
try(lines(sort(adjpSDorqa[, 2]), col=1, lwd=2, lty=1, type="s"), TRUE)
try(lines(sort(adjpHolmorqa[, 2]), col=2,lwd=2, lty=2, type="s"), TRUE)
try(lines(sort(adjpHochorqa[, 2]), col=3,lwd=2, lty=2, type="s"), TRUE)
try(lines(sort(adjpBonorqa[, 2]), col=4, lwd=2, lty=2, type="s"), TRUE)
try(lines(sort(pval.orQA), col=2, lwd=2, lty=1, type="s"))
abline(FDRval, 0)
metd <- result3[, 1]
col <- result3[, 3]
type <- result3[, 4]
legend((0.7*nrow(exprs2orqa)), 0.62, c("Raw P-val",metd),
col = c(2, as.numeric(col)), lty = c(1, as.numeric(type)), lwd = 2, merge = TRUE )
options(warn = 1)
}
}
Plot2(rankPlot, 1.7, 1.5, title="Windows Graph Output: Plot p-values")
}
if (cbVal11=="1") {
PVALSvsDiffPlot <- function () {
params <- par(bg="white")
options(show.error.messages = FALSE)
x <- cbind(Mu.Diff, -log(pval.orQA))
colors <- densCols(x)
plot (x,col=colors, pch=20, lwd=3,ylab="- log p-values", xlab="Fold change" )
}
Plot2(PVALSvsDiffPlot, 1.5, 1.5, title="Windows Graph Output: Fold change vs p-values" )
## Fold change = > Mu*dose.max-Mu*dose.min ##
}
tkconfigure(orqa, cursor="arrow")
options(show.error.messages = TRUE)
}
}
plot.but <-tkbutton(frame3,text=" Produce plots ", command=PlotBut)
tkgrid(tklabel(frame3,text=" "), plot.but)
tkgrid(frame3)
tkgrid.configure(frame3,sticky="nsw")
onExit <- function(){
ReturnVal <<- 0
tkdestroy(orqa)
}
tkgrid(tklabel(buttonFrameasym, text=" "))
Exit.but <- tkbutton(buttonFrameasym, text=" Exit the analysis ", command=onExit )
tkgrid(Exit.but)
tkgrid.configure(Exit.but, sticky="e")
tkgrid(spec.frm)
tkgrid(buttonFrameasym)
}
}
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