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R/ExactE2.R
In IsoGeneGUI: A graphical user interface to conduct a dose-response analysis of microarray data
Defines functions
`ExactE2`
`ExactE2` <-
function()
## Asymp in this function corresponds to exact pvalues ##
{
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 {
asym<-tktoplevel()
tkwm.title(asym,"Global Likelihood Ratio Test (E2) Analysis: Asymptotic")
spec.frm <- tkframe(asym,borderwidth=2)
frame1 <- tkframe(spec.frm, relief="groove", borderwidth=2)
buttonFrameasym <-tkframe(asym,borderwidth=2)
### Select genes ##
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 )
Calc.Asymp <- 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(asym)
}
else {
tkconfigure(asym,cursor="watch")
rbVal1 <- as.character(tclvalue(rbValue1))
if (rbVal1=="all") {
exprs2Asymp <<- exprs
matchID <- c(1:nrow(exprs2Asymp ))
}
if (rbVal1=="range") {
exprs2Asymp <<- exprs [tclvalue(fromgene):tclvalue(togene),]
matchID <- c(tclvalue(fromgene):tclvalue(togene))
}
assign("matchIDAsymp",matchID ,envir=.GlobalEnv)
# foldchange ##
res.Asymp <<-ExactE2Val(dose,exprs2Asymp )
pval.Asymp <<- res.Asymp[,2]
ProbeID <<- rownames(exprs2Asymp)
Mu.Diff.Asymp <<- MeanDiff (dose,exprs2Asymp)
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(asym)
tkconfigure(asym,cursor="arrow")
try(tkdelete(treeWidget,"nodeAsymp") , silent = T )
try( tkdelete(treeWidget,"AsymPvalNode"), silent = T )
tkinsert(treeWidget,"end","Record2Node","AsymPvalNode",text="Raw P-values")
tkinsert(treeWidget,"end","AsymPvalNode","NumGeneNode",text=paste("Number gene analyzed: ",N) )
}
}
Calculate.but <-tkbutton(frame1,text=" Calculate ",command=Calc.Asymp)
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,
tklabel(frame1,text=" "),Calculate.but)
tkgrid.configure(rb2,sticky="w")
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.Asymp"))
{
ReturnVal <- tkmessageBox(title="Error Message",message="The raw-pvalues have been not calculated yet!",icon="info",type="ok")
if (tclvalue(ReturnVal)== "ok") tkfocus(asym)
}
else {
tkconfigure(asym,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 <- E2Val.Asymp
FDRval <<- as.numeric(tclvalue(FDR))
Direction <- res.Asymp[,3]
try( tkdelete(treeWidget,"AdjPvalNode"), silent = T )
tkinsert(treeWidget,"end","Record2Node","AdjPvalNode",text= paste("Adjusted P-values, FDR: ", FDRval) )
sigeneBH <<- sigeneBY <<- sigeneSS <<- sigeneSD <<- sigeneHolm <<- sigeneHoch <<- sigeneBon <<- NULL
adjpBH <<- adjpBY <<- adjpSS <<- adjpSD <<- adjpHolm <<- adjpHoch <<- adjpBon <<- NULL
result <- matrix(NA,7,4)
if (cbVal1=="1") {
adjpBH <- adjustment (pval.Asymp,"BH")
assign("adjpBH",adjpBH ,envir=.GlobalEnv)
sigeneBH <- Signif (pval.Asymp, FDRval ,"BH")
numsigBH <- nrow(sigeneBH )
numsigBH [is.null(numsigBH )] <- 0
result[1,] <- c("BH",numsigBH,1,1 )
tkinsert(treeWidget,"end","AdjPvalNode","BHNode",text= paste("BH, Sig:", numsigBH ) )
}
if (cbVal2=="1") {
adjpBY <- adjustment (pval.Asymp,"BY")
assign("adjpBY",adjpBY ,envir=.GlobalEnv)
sigeneBY <- Signif (pval.Asymp, FDRval ,"BY")
numsigBY <- nrow(sigeneBY )
numsigBY[is.null(numsigBY)] <- 0
result[2,] <- c("BY",numsigBY ,3,1)
tkinsert(treeWidget,"end","AdjPvalNode","BYNode",text= paste("BY, Sig:", numsigBY ) )
}
if (cbVal3=="1") {
adjpSS <- adjustment (pval.Asymp,"SidakSS")
assign("adjpSS",adjpSS ,envir=.GlobalEnv)
sigeneSS <- Signif (pval.Asymp, FDRval ,"SidakSS")
numsigSS <- nrow(sigeneSS )
numsigSS [is.null(numsigSS )] <- 0
result[3,] <- c("SidakSS",numsigSS,4,1 )
tkinsert(treeWidget,"end","AdjPvalNode","Sidak1Node",text= paste ("Sidak SS, Sig:", numsigSS ) )
}
if (cbVal4=="1") {
adjpSD <- adjustment (pval.Asymp,"SidakSD")
assign("adjpSD",adjpSD,envir=.GlobalEnv)
sigeneSD <- Signif (pval.Asymp, FDRval ,"SidakSD")
numsigSD <- nrow(sigeneSD )
numsigSD [is.null(numsigSD )] <- 0
result[4,] <- c("SidakSD",numsigSD,1,2 )
tkinsert(treeWidget,"end","AdjPvalNode","Sidak2Node",text= paste ("Sidak SD, Sig:", numsigSD ) )
}
if (cbVal5=="1") {
adjpHolm <- adjustment (pval.Asymp,"Holm")
assign("adjpHolm",adjpHolm,envir=.GlobalEnv)
sigeneHolm <- Signif (pval.Asymp, FDRval ,"Holm")
numsigHolm <- nrow(sigeneHolm )
numsigHolm [is.null(numsigHolm )] <- 0
result[5,] <- c("Holm",numsigHolm,2,2 )
tkinsert(treeWidget,"end","AdjPvalNode","HolmNode",text= paste( "Holm, Sig:", numsigHolm ) )
}
if (cbVal6=="1") {
adjpHoch <- adjustment (pval.Asymp,"Hochberg")
assign("adjpHoch",adjpHoch ,envir=.GlobalEnv)
sigeneHoch <- Signif (pval.Asymp, FDRval ,"Hochberg")
numsigHoch <- nrow(sigeneHoch)
numsigHoch [is.null(numsigHoch )] <- 0
result[6,] <- c("Hochberg",numsigHoch , 3,2 )
tkinsert(treeWidget,"end","AdjPvalNode","HocbergNode",text= paste ("Hocberg, Sig:", numsigHoch ) )
}
if (cbVal7=="1") {
adjpBon <- adjustment (pval.Asymp,"Bonferroni")
assign("adjpBon",adjpBon ,envir=.GlobalEnv)
sigeneBon <- Signif (pval.Asymp, FDRval ,"Bonferroni")
numsigBon <- nrow(sigeneBon)
numsigBon [is.null(numsigBon )] <- 0
result[7,] <- c("Bonferroni",numsigBon ,4,2 )
tkinsert(treeWidget,"end","AdjPvalNode","BonferroniNode",text=paste("Bonferroni, Sig:", numsigBon ) )
}
num <- nrow(exprs2Asymp )
result2 <- na.exclude(result)
colnames(result2) <- c("P-values Adjusment","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 )
printExact(num,FDRval ,result2)
RowNumSig <- unique(c(sigeneBH$row.num,sigeneBY$row.num,sigeneSS$row.num,sigeneSD$row.num,
sigeneHolm$row.num,sigeneHoch$row.num,sigeneBon$row.num) )
AdjPvalAll <- cbind(adjpBH[,2], adjpBY[,2],adjpSS[,2],adjpSD[,2],adjpHolm[,2],adjpHoch[,2],adjpBon [,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)
Mu.Diff <- Mu.Diff.Asymp
row.num <- 1:nrow(exprs2Asymp)
Res.Asymtot <<- data.frame(ProbeID, row.num, Mu.Diff,Direction, E2Val, pval.Asymp,AdjPvalAll)
rownames(Res.Asymtot) <<- NULL
AsymtotSigGenes1 <- Res.Asymtot[orderedRowNum,]
rownames(AsymtotSigGenes1) <- NULL
SigGenes.AsymptotE2 <<- AsymtotSigGenes1
if(cbVal10=="1" ) {
try(showData(AsymtotSigGenes1 ,title= paste("List of Significant Genes based on exact P-values, FDR:", FDRval ," Number of Genes analyzed :",num)))
}
tkconfigure(asym,cursor="arrow")
result3 <- result2
assign("result3",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.AsymptotE2)
}
savesiggene.but <- tkbutton(frame2,text="Save significant genes", command=savesiggene)
saveallgene <- function() {
Pval.AllGenes.Asymp <<- Res.Asymtot
save.result("Pval.AllGenes.Asymp")
}
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)
cb8 <- tkcheckbutton(frame3)
cb9 <- tkcheckbutton(frame3)
cb11 <- tkcheckbutton(frame3)
cbValue8 <- tclVar("0")
cbValue9 <- tclVar("0")
cbValue11 <- tclVar("0")
tkconfigure(cb8,variable=cbValue8,text="Plot E2 values vs raw p-values")
tkconfigure(cb9,variable=cbValue9,text="Ranking Plot (Adjust the p-values first)")
tkconfigure(cb11,variable=cbValue11,text="Plot Fold change vs E2")
label.plots <-tklabel(frame3,text="Plots: ")
tkgrid(label.plots )
tkgrid.configure(label.plots,sticky="w")
tkgrid.configure(cb8,sticky="w")
tkgrid.configure(cb11,sticky="w")
tkgrid.configure(cb9,sticky="w")
tkgrid(cb8)
tkgrid(cb10)
tkgrid(cb9)
PlotBut <- function () {
if (!exists("pval.Asymp"))
{
ReturnVal <- tkmessageBox(title="Error Message",message="The raw-pvalues have not calculated yet!",icon="info",type="ok")
if (tclvalue(ReturnVal)== "ok") tkfocus(asym)
}
else {
tkconfigure(asym,cursor="watch")
cbVal8 <- as.character(tclvalue(cbValue8))
cbVal9 <- as.character(tclvalue(cbValue9))
cbVal11 <- as.character(tclvalue(cbValue11))
if (cbVal8=="1"){
rankPlot <- function()
{
params <- par(bg="white")
x <-cbind(res.Asymp[,1],-log10(pval.Asymp))
colors <- densCols(x)
plot(x, col=colors, pch=20, lwd=3,xlab=" E2 ",
ylab="-log10(Raw P-values)")
}
Plot2(rankPlot,1.5,1.5, title="Windows Graph Output: E2 vs -log10(raw p-value) Plot" )
}
if (cbVal9=="1" ){
rankPlot <- function()
{
if (!exists("result3")) {
params <- par(bg="white")
options(show.error.messages = FALSE)
plot((1:nrow(exprs2Asymp )),main="P-values",xlab=" Index ",ylab="Raw P-values",ylim=c(0,1))
try(lines(sort(pval.Asymp),col=2, lwd=2,lty=1,type="s"))
}
else{
params <- par(bg="white")
options(warn = -1)
plot((1:nrow(exprs2Asymp )),main="P-values",xlab=" Index ",ylab="P-values",ylim=c(0,1))
try(lines(sort(adjpBH[,2] ),col=1, lwd=2,lty=1,type="s"),T)
try(lines(sort(adjpBY[,2] ),col=3, lwd=2,lty=1,type="s"),T)
try(lines(sort(adjpSS[,2] ),col=4, lwd=2,lty=1,type="s"),T)
try(lines(sort(adjpSD[,2] ),col=1, lwd=2,lty=1,type="s"),T)
try(lines(sort(adjpHolm[,2] ),col=2, lwd=2,lty=2,type="s"),T)
try(lines(sort(adjpHoch[,2] ),col=3, lwd=2,lty=2,type="s"),T)
try(lines(sort(adjpBon[,2] ),col=4, lwd=2,lty=2,type="s"),T)
try(lines(sort(pval.Asymp),col=2, lwd=2,lty=1,type="s"))
abline(FDRval ,0)
metd <- result3[,1]
col <- result3[,3]
type <- result3[,4]
legend((0.6*nrow(exprs2Asymp )), 0.9, 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") {
E2vsDiffPlot <- function () {
params <- par(bg="white")
options(show.error.messages = FALSE)
x <-cbind( Mu.Diff.Asymp ,res.Asymp[,1] )
colors <- densCols(x)
plot (x,col=colors, pch=20, lwd=3,ylab="E2", xlab="Fold change" )
}
Plot2(E2vsDiffPlot ,1.5,1.5, title="Windows Graph Output: Fold change vs E2" )
## Fold change = > Mu*dose.max-Mu*dose.min ##
}
tkconfigure(asym,cursor="arrow")
options(show.error.messages = T)
}
}
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(asym)
}
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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Defines functions `ExactE2`
`ExactE2` <-
function()
## Asymp in this function corresponds to exact pvalues ##
{
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 {
asym<-tktoplevel()
tkwm.title(asym,"Global Likelihood Ratio Test (E2) Analysis: Asymptotic")
spec.frm <- tkframe(asym,borderwidth=2)
frame1 <- tkframe(spec.frm, relief="groove", borderwidth=2)
buttonFrameasym <-tkframe(asym,borderwidth=2)
### Select genes ##
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 )
Calc.Asymp <- 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(asym)
}
else {
tkconfigure(asym,cursor="watch")
rbVal1 <- as.character(tclvalue(rbValue1))
if (rbVal1=="all") {
exprs2Asymp <<- exprs
matchID <- c(1:nrow(exprs2Asymp ))
}
if (rbVal1=="range") {
exprs2Asymp <<- exprs [tclvalue(fromgene):tclvalue(togene),]
matchID <- c(tclvalue(fromgene):tclvalue(togene))
}
assign("matchIDAsymp",matchID ,envir=.GlobalEnv)
# foldchange ##
res.Asymp <<-ExactE2Val(dose,exprs2Asymp )
pval.Asymp <<- res.Asymp[,2]
ProbeID <<- rownames(exprs2Asymp)
Mu.Diff.Asymp <<- MeanDiff (dose,exprs2Asymp)
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(asym)
tkconfigure(asym,cursor="arrow")
try(tkdelete(treeWidget,"nodeAsymp") , silent = T )
try( tkdelete(treeWidget,"AsymPvalNode"), silent = T )
tkinsert(treeWidget,"end","Record2Node","AsymPvalNode",text="Raw P-values")
tkinsert(treeWidget,"end","AsymPvalNode","NumGeneNode",text=paste("Number gene analyzed: ",N) )
}
}
Calculate.but <-tkbutton(frame1,text=" Calculate ",command=Calc.Asymp)
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,
tklabel(frame1,text=" "),Calculate.but)
tkgrid.configure(rb2,sticky="w")
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.Asymp"))
{
ReturnVal <- tkmessageBox(title="Error Message",message="The raw-pvalues have been not calculated yet!",icon="info",type="ok")
if (tclvalue(ReturnVal)== "ok") tkfocus(asym)
}
else {
tkconfigure(asym,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 <- E2Val.Asymp
FDRval <<- as.numeric(tclvalue(FDR))
Direction <- res.Asymp[,3]
try( tkdelete(treeWidget,"AdjPvalNode"), silent = T )
tkinsert(treeWidget,"end","Record2Node","AdjPvalNode",text= paste("Adjusted P-values, FDR: ", FDRval) )
sigeneBH <<- sigeneBY <<- sigeneSS <<- sigeneSD <<- sigeneHolm <<- sigeneHoch <<- sigeneBon <<- NULL
adjpBH <<- adjpBY <<- adjpSS <<- adjpSD <<- adjpHolm <<- adjpHoch <<- adjpBon <<- NULL
result <- matrix(NA,7,4)
if (cbVal1=="1") {
adjpBH <- adjustment (pval.Asymp,"BH")
assign("adjpBH",adjpBH ,envir=.GlobalEnv)
sigeneBH <- Signif (pval.Asymp, FDRval ,"BH")
numsigBH <- nrow(sigeneBH )
numsigBH [is.null(numsigBH )] <- 0
result[1,] <- c("BH",numsigBH,1,1 )
tkinsert(treeWidget,"end","AdjPvalNode","BHNode",text= paste("BH, Sig:", numsigBH ) )
}
if (cbVal2=="1") {
adjpBY <- adjustment (pval.Asymp,"BY")
assign("adjpBY",adjpBY ,envir=.GlobalEnv)
sigeneBY <- Signif (pval.Asymp, FDRval ,"BY")
numsigBY <- nrow(sigeneBY )
numsigBY[is.null(numsigBY)] <- 0
result[2,] <- c("BY",numsigBY ,3,1)
tkinsert(treeWidget,"end","AdjPvalNode","BYNode",text= paste("BY, Sig:", numsigBY ) )
}
if (cbVal3=="1") {
adjpSS <- adjustment (pval.Asymp,"SidakSS")
assign("adjpSS",adjpSS ,envir=.GlobalEnv)
sigeneSS <- Signif (pval.Asymp, FDRval ,"SidakSS")
numsigSS <- nrow(sigeneSS )
numsigSS [is.null(numsigSS )] <- 0
result[3,] <- c("SidakSS",numsigSS,4,1 )
tkinsert(treeWidget,"end","AdjPvalNode","Sidak1Node",text= paste ("Sidak SS, Sig:", numsigSS ) )
}
if (cbVal4=="1") {
adjpSD <- adjustment (pval.Asymp,"SidakSD")
assign("adjpSD",adjpSD,envir=.GlobalEnv)
sigeneSD <- Signif (pval.Asymp, FDRval ,"SidakSD")
numsigSD <- nrow(sigeneSD )
numsigSD [is.null(numsigSD )] <- 0
result[4,] <- c("SidakSD",numsigSD,1,2 )
tkinsert(treeWidget,"end","AdjPvalNode","Sidak2Node",text= paste ("Sidak SD, Sig:", numsigSD ) )
}
if (cbVal5=="1") {
adjpHolm <- adjustment (pval.Asymp,"Holm")
assign("adjpHolm",adjpHolm,envir=.GlobalEnv)
sigeneHolm <- Signif (pval.Asymp, FDRval ,"Holm")
numsigHolm <- nrow(sigeneHolm )
numsigHolm [is.null(numsigHolm )] <- 0
result[5,] <- c("Holm",numsigHolm,2,2 )
tkinsert(treeWidget,"end","AdjPvalNode","HolmNode",text= paste( "Holm, Sig:", numsigHolm ) )
}
if (cbVal6=="1") {
adjpHoch <- adjustment (pval.Asymp,"Hochberg")
assign("adjpHoch",adjpHoch ,envir=.GlobalEnv)
sigeneHoch <- Signif (pval.Asymp, FDRval ,"Hochberg")
numsigHoch <- nrow(sigeneHoch)
numsigHoch [is.null(numsigHoch )] <- 0
result[6,] <- c("Hochberg",numsigHoch , 3,2 )
tkinsert(treeWidget,"end","AdjPvalNode","HocbergNode",text= paste ("Hocberg, Sig:", numsigHoch ) )
}
if (cbVal7=="1") {
adjpBon <- adjustment (pval.Asymp,"Bonferroni")
assign("adjpBon",adjpBon ,envir=.GlobalEnv)
sigeneBon <- Signif (pval.Asymp, FDRval ,"Bonferroni")
numsigBon <- nrow(sigeneBon)
numsigBon [is.null(numsigBon )] <- 0
result[7,] <- c("Bonferroni",numsigBon ,4,2 )
tkinsert(treeWidget,"end","AdjPvalNode","BonferroniNode",text=paste("Bonferroni, Sig:", numsigBon ) )
}
num <- nrow(exprs2Asymp )
result2 <- na.exclude(result)
colnames(result2) <- c("P-values Adjusment","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 )
printExact(num,FDRval ,result2)
RowNumSig <- unique(c(sigeneBH$row.num,sigeneBY$row.num,sigeneSS$row.num,sigeneSD$row.num,
sigeneHolm$row.num,sigeneHoch$row.num,sigeneBon$row.num) )
AdjPvalAll <- cbind(adjpBH[,2], adjpBY[,2],adjpSS[,2],adjpSD[,2],adjpHolm[,2],adjpHoch[,2],adjpBon [,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)
Mu.Diff <- Mu.Diff.Asymp
row.num <- 1:nrow(exprs2Asymp)
Res.Asymtot <<- data.frame(ProbeID, row.num, Mu.Diff,Direction, E2Val, pval.Asymp,AdjPvalAll)
rownames(Res.Asymtot) <<- NULL
AsymtotSigGenes1 <- Res.Asymtot[orderedRowNum,]
rownames(AsymtotSigGenes1) <- NULL
SigGenes.AsymptotE2 <<- AsymtotSigGenes1
if(cbVal10=="1" ) {
try(showData(AsymtotSigGenes1 ,title= paste("List of Significant Genes based on exact P-values, FDR:", FDRval ," Number of Genes analyzed :",num)))
}
tkconfigure(asym,cursor="arrow")
result3 <- result2
assign("result3",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.AsymptotE2)
}
savesiggene.but <- tkbutton(frame2,text="Save significant genes", command=savesiggene)
saveallgene <- function() {
Pval.AllGenes.Asymp <<- Res.Asymtot
save.result("Pval.AllGenes.Asymp")
}
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)
cb8 <- tkcheckbutton(frame3)
cb9 <- tkcheckbutton(frame3)
cb11 <- tkcheckbutton(frame3)
cbValue8 <- tclVar("0")
cbValue9 <- tclVar("0")
cbValue11 <- tclVar("0")
tkconfigure(cb8,variable=cbValue8,text="Plot E2 values vs raw p-values")
tkconfigure(cb9,variable=cbValue9,text="Ranking Plot (Adjust the p-values first)")
tkconfigure(cb11,variable=cbValue11,text="Plot Fold change vs E2")
label.plots <-tklabel(frame3,text="Plots: ")
tkgrid(label.plots )
tkgrid.configure(label.plots,sticky="w")
tkgrid.configure(cb8,sticky="w")
tkgrid.configure(cb11,sticky="w")
tkgrid.configure(cb9,sticky="w")
tkgrid(cb8)
tkgrid(cb10)
tkgrid(cb9)
PlotBut <- function () {
if (!exists("pval.Asymp"))
{
ReturnVal <- tkmessageBox(title="Error Message",message="The raw-pvalues have not calculated yet!",icon="info",type="ok")
if (tclvalue(ReturnVal)== "ok") tkfocus(asym)
}
else {
tkconfigure(asym,cursor="watch")
cbVal8 <- as.character(tclvalue(cbValue8))
cbVal9 <- as.character(tclvalue(cbValue9))
cbVal11 <- as.character(tclvalue(cbValue11))
if (cbVal8=="1"){
rankPlot <- function()
{
params <- par(bg="white")
x <-cbind(res.Asymp[,1],-log10(pval.Asymp))
colors <- densCols(x)
plot(x, col=colors, pch=20, lwd=3,xlab=" E2 ",
ylab="-log10(Raw P-values)")
}
Plot2(rankPlot,1.5,1.5, title="Windows Graph Output: E2 vs -log10(raw p-value) Plot" )
}
if (cbVal9=="1" ){
rankPlot <- function()
{
if (!exists("result3")) {
params <- par(bg="white")
options(show.error.messages = FALSE)
plot((1:nrow(exprs2Asymp )),main="P-values",xlab=" Index ",ylab="Raw P-values",ylim=c(0,1))
try(lines(sort(pval.Asymp),col=2, lwd=2,lty=1,type="s"))
}
else{
params <- par(bg="white")
options(warn = -1)
plot((1:nrow(exprs2Asymp )),main="P-values",xlab=" Index ",ylab="P-values",ylim=c(0,1))
try(lines(sort(adjpBH[,2] ),col=1, lwd=2,lty=1,type="s"),T)
try(lines(sort(adjpBY[,2] ),col=3, lwd=2,lty=1,type="s"),T)
try(lines(sort(adjpSS[,2] ),col=4, lwd=2,lty=1,type="s"),T)
try(lines(sort(adjpSD[,2] ),col=1, lwd=2,lty=1,type="s"),T)
try(lines(sort(adjpHolm[,2] ),col=2, lwd=2,lty=2,type="s"),T)
try(lines(sort(adjpHoch[,2] ),col=3, lwd=2,lty=2,type="s"),T)
try(lines(sort(adjpBon[,2] ),col=4, lwd=2,lty=2,type="s"),T)
try(lines(sort(pval.Asymp),col=2, lwd=2,lty=1,type="s"))
abline(FDRval ,0)
metd <- result3[,1]
col <- result3[,3]
type <- result3[,4]
legend((0.6*nrow(exprs2Asymp )), 0.9, 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") {
E2vsDiffPlot <- function () {
params <- par(bg="white")
options(show.error.messages = FALSE)
x <-cbind( Mu.Diff.Asymp ,res.Asymp[,1] )
colors <- densCols(x)
plot (x,col=colors, pch=20, lwd=3,ylab="E2", xlab="Fold change" )
}
Plot2(E2vsDiffPlot ,1.5,1.5, title="Windows Graph Output: Fold change vs E2" )
## Fold change = > Mu*dose.max-Mu*dose.min ##
}
tkconfigure(asym,cursor="arrow")
options(show.error.messages = T)
}
}
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(asym)
}
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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