Nothing
R/qcmenu.R
In oneChannelGUI: A graphical interface designed to facilitate analysis of microarrays and miRNA/RNA-seq data on laptops
Defines functions
delta.plot1
PlotOptionsv1
affyPlotMA
Documented in
affyPlotMA
PlotOptionsv1
#set of functions, directly/indirectly involved, in oneChannelGUI qcMenu
#oneChannelGUI normBoxplot this function produces a boxplot for NormalizedAffyData
#oneChannelGUI ocPlotPCA this function produces a PCA plot using the normalized expression data works both with affy and exon arrays
#oneChannelGUI ocPlotHist this function produces an affy hist plot for exon and gene level data after probeset intenisty calculation
#oneChannelGUI sample.size.evaluation allows sample size and statistical power estimation using the ssize package
#oneChannelGUI sample.size.evaluation1 allows sample size and statistical power estimation using the sizepower package
#oneChannelGUI PlotOptionsv1 plotting optino selections
#affyPlotMA modified to use the expr(NormalizedAffyData)
#oneChannelGUI rawBoxplotPN plot the raw log2 intensity values for positive and negative ctrls extracted from CEL files
#oneChannelGUI qcMDS evaluating the presence eof outliers using plotMDS.dge of NGS data
#oneChannelGUI EDAplotQuality bam qc associated to EDASeq
# EDAreadNumber
# EDANtFreq
# EDAboxplot
# EDAbiasPlot
# oneChannelGUI fastQC java tool to evaluate fastq quality
################################################################################
"normBoxplot" <- function(){
#error if no data are loaded
Try(whichArrayPlatform <- get("whichArrayPlatform",envir=affylmGUIenvironment))
if(whichArrayPlatform ==""){
Try(tkmessageBox(title="QC",message="No arrays have been loaded. Please try New or Open from the File menu.",type="ok",icon="error"))
Try(tkfocus(.affylmGUIglobals$ttMain))
Try(return())
}
#########################
if(whichArrayPlatform=="LARGE" || whichArrayPlatform=="GENE" || whichArrayPlatform=="ILLU"){
if(affylmGUIenvironment$NormalizedAffyData.Available){
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="watch"))
Try(NormalizedAffyData <- get("NormalizedAffyData",envir=affylmGUIenvironment))
Try( boxplot(as.data.frame(exprs(NormalizedAffyData)), las=2, names=pData(NormalizedAffyData)$Name,ylab="Normalized log2(intensities)"))
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="arrow"))
}
} else if (whichArrayPlatform=="AFFY"){
if(affylmGUIenvironment$NormalizedAffyData.Available){
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="watch"))
Try(NormalizedAffyData <- get("NormalizedAffyData",envir=affylmGUIenvironment))
Try( boxplot(as.data.frame(exprs(NormalizedAffyData)), las=2, names=pData(NormalizedAffyData)$Name,ylab="Normalized log2(intensities)"))
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="arrow"))
}
} else if (whichArrayPlatform=="NGS"){
if(affylmGUIenvironment$NormalizedAffyData.Available){
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="watch"))
Try(NormalizedAffyData <- get("NormalizedAffyData",envir=affylmGUIenvironment))
Try( boxplot(as.data.frame(log10(exprs(NormalizedAffyData))), las=2, names=pData(NormalizedAffyData)$Name,ylab="log10 peaks counts"))
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="arrow"))
}
} else{
Try(tkmessageBox(title="Box plot normalized data",message="Probe set summary is not available!\nNext menu will give options for probe set summarization", type="ok", icon="info"))
Try(NormalizeNow())
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="watch"))
Try(NormalizedAffyData <- get("NormalizedAffyData",envir=affylmGUIenvironment))
Try( boxplot(as.data.frame(exprs(NormalizedAffyData)), las=2, names=pData(NormalizedAffyData)$Name,ylab="Normalized log2(intensities)"))
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="arrow"))
}
}
################################################################################
#run the affycoretool plotPCA
"ocPlotPCA" <- function(){
#error if no data are loaded
Try(whichArrayPlatform <- get("whichArrayPlatform",envir=affylmGUIenvironment))
if(whichArrayPlatform ==""){
Try(tkmessageBox(title="QC",message="No arrays have been loaded. Please try New or Open from the File menu.",type="ok",icon="error"))
Try(tkfocus(.affylmGUIglobals$ttMain))
Try(return())
}
#########################
#plotPCA was derived by affycoretools they desapeared in relase 2.0
"plotPCA" <- function (eset, groups = NULL, groupnames = NULL, addtext = NULL,
x.coord = NULL, y.coord = NULL, screeplot = FALSE, squarepca = FALSE,
pch = NULL, col = NULL, title=NULL,...) {
if (is.null(groupnames)) groupnames <- sampleNames(eset)
if (is.factor(groupnames)) groupnames <- as.character(groupnames)
pca <- prcomp(t(exprs(eset)))
x <- exprs(eset)
dimnames(x)[[2]] <- groupnames
hc <- hclust(dist(t(x)), "ave")
if (screeplot) {
plot(pca, main = title)
} else {
if (squarepca) {
ylim <- max(abs(range(pca$x[, 1])))
ylim <- c(-ylim, ylim)
} else ylim <- NULL
if (!is.null(groups)) {
if (is.null(pch)) pch <- groups
if (is.null(col)) col <- groups
plot(pca$x[, 1:2], pch = pch, col = col, ylab = "PC2", xlab = "PC1", main = title, ylim = ylim, ...)
} else {
if (is.null(pch)) pch <- ""
if (is.null(col)) col <- 1:length(groupnames)
par(mfrow=c(1,3))
plot(pca, main="PCs information content")
plot(pca$x[, 1:2], pch = pch, ylab = "PC2", xlab = "PC1", main = title, ylim = ylim, ...)
text(pca$x[, 1:2], groupnames, col= col <- 1:length(groupnames) , cex=0.7)
plot(hc, main="Samples HCL", xlab="")
}
}
}
Try(whichArrayPlatform <- get("whichArrayPlatform",envir=affylmGUIenvironment))
if(whichArrayPlatform=="EXON"){
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="watch"))
if(affylmGUIenvironment$exonAffyData.Available){
##makning the menu for selecting gene or exon level density plot
Try(ttGeneExonMethod <- tktoplevel(.affylmGUIglobals$ttMain))
Try(tkwm.deiconify(ttGeneExonMethod))
Try(tkgrab.set(ttGeneExonMethod))
Try(tkfocus(ttGeneExonMethod))
Try(tkwm.title(ttGeneExonMethod,"Gene/Exon level plots"))
Try(tkgrid(tklabel(ttGeneExonMethod,text=" ")))
Try(ttGeneExonMethodTcl <- tclVar("gene"))
Try(rbGene <- tkradiobutton(ttGeneExonMethod,text="Gene levels",variable=ttGeneExonMethodTcl,value="gene",font=.affylmGUIglobals$affylmGUIfont2))
Try(rbExon<-tkradiobutton(ttGeneExonMethod,text="Exon levels",variable=ttGeneExonMethodTcl,value="exon",font=.affylmGUIglobals$affylmGUIfont2))
Try(tkgrid(tklabel(ttGeneExonMethod,text=" "),rbGene))
Try(tkgrid(tklabel(ttGeneExonMethod,text=" "),rbExon))
Try(tkgrid.configure(rbGene,rbExon,columnspan=2,sticky="w"))
Try(tkgrid(tklabel(ttGeneExonMethod,text=" "),tklabel(ttGeneExonMethod,text=" ")))
Try(ReturnVal <- "")
Try(onCancel <- function() {Try(ReturnVal <<- "");Try(tkgrab.release(ttGeneExonMethod));Try(tkdestroy(ttGeneExonMethod));Try(tkfocus(.affylmGUIglobals$ttMain))})
Try(onOK <- function() {Try(ReturnVal <<- tclvalue(ttGeneExonMethodTcl));Try(tkgrab.release(ttGeneExonMethod));Try(tkdestroy(ttGeneExonMethod));Try(tkfocus(.affylmGUIglobals$ttMain))})
Try(OK.but <- tkbutton(ttGeneExonMethod,text="OK",command=onOK,font=.affylmGUIglobals$affylmGUIfont2))
Try(Cancel.but <- tkbutton(ttGeneExonMethod,text="Cancel",command=onCancel,font=.affylmGUIglobals$affylmGUIfont2))
Try(tkgrid(tklabel(ttGeneExonMethod,text=" "),OK.but,Cancel.but,tklabel(ttGeneExonMethod,text=" ")))
Try(tkgrid.configure(OK.but,sticky="e"))
Try(tkgrid.configure(Cancel.but,sticky="w"))
Try(tkgrid(tklabel(ttGeneExonMethod,text=" ")))
Try(tkbind(ttGeneExonMethod,"<Destroy>",function() {ReturnVal <- "";Try(tkgrab.release(ttGeneExonMethod));Try(tkfocus(.affylmGUIglobals$ttMain));}))
Try(tkbind(OK.but, "<Return>",onOK))
Try(tkbind(Cancel.but, "<Return>",onCancel))
Try(tkwait.window(ttGeneExonMethod))
if(ReturnVal=="gene"){
Try(NormalizedAffyData <- get("NormalizedAffyData",envir=affylmGUIenvironment))
Try(plotPCA(NormalizedAffyData, groupnames= affylmGUIenvironment$Targets$Name, title="Gene level PCA"))
} else if (ReturnVal=="exon"){
Try(exonAffyData <- get("exonAffyData",envir=affylmGUIenvironment))
Try(plotPCA(exonAffyData, groupnames= affylmGUIenvironment$Targets$Name, title="Exon level PCA"))
} else {
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="arrow"))
Try(return())
}
} else{
Try(tkmessageBox(title="Gene level PCA/HCL",message="No exon data are available! These data seem not to be exon arrays data",type="ok",icon="error"))
}
Try(tkmessageBox(title="Exon level PCA/HCL",message=paste("Plots will be displayed in the main R window")))
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="arrow"))
}
if(whichArrayPlatform=="AFFY"){
if(affylmGUIenvironment$NormalizedAffyData.Available){
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="watch"))
Try(NormalizedAffyData <- get("NormalizedAffyData",envir=affylmGUIenvironment))
Try(plotPCA(NormalizedAffyData, groupnames= affylmGUIenvironment$Targets$Name, title="Samples PCA plot"))
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="arrow"))
} else{
Try(tkmessageBox(title="plotPCA",message="Probe set summary is not available!\nNext menu will give options for probe set summarization", type="ok", icon="info"))
Try(NormalizeNow())
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="watch"))
Try(NormalizedAffyData <- get("NormalizedAffyData",envir=affylmGUIenvironment))
Try(plotPCA(NormalizedAffyData, groupnames= affylmGUIenvironment$Targets$Name, title="Samples PCA plot"))
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="arrow"))
}
}
if(whichArrayPlatform=="LARGE" || whichArrayPlatform=="GENE" || whichArrayPlatform=="ILLU" || whichArrayPlatform=="NGS"){
if(affylmGUIenvironment$NormalizedAffyData.Available){
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="watch"))
Try(NormalizedAffyData <- get("NormalizedAffyData",envir=affylmGUIenvironment))
Try(plotPCA(NormalizedAffyData, groupnames= affylmGUIenvironment$Targets$Name, title="Samples PCA plot"))
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="arrow"))
} else{
Try(tkmessageBox(title="plotPCA",message="Probe set summary is not available!", type="ok", icon="error"))
}
}
}
################################################################################
#this function will plot density plot for the gene and exon expression loaded in oneChannelGUI
#modify plotHist function from affycoretools
"ocPlotHist" <- function(){
#error if no data are loaded
Try(whichArrayPlatform <- get("whichArrayPlatform",envir=affylmGUIenvironment))
if(whichArrayPlatform ==""){
Try(tkmessageBox(title="QC",message="No arrays have been loaded. Please try New or Open from the File menu.",type="ok",icon="error"))
Try(tkfocus(.affylmGUIglobals$ttMain))
Try(return())
}
#########################
plotHist<- function (dat, filenames = NULL, title=NULL)
{
if (is.null(filenames))
filenames <- sampleNames(dat)
cl <- make.cl(filenames)
if (length(filenames) <= 8) {
if (is(dat, "ExpressionSet"))
plotDensity(as.matrix(exprs(dat)), lty = cl, lwd = 2, col = 1:length(filenames), main=title)
x.ax <- legend(1, 1, legend = filenames, lty = 1, lwd = 2,
col = cl, plot = FALSE)$rect$w
legend(par("usr")[2] - (par("usr")[2] - par("usr")[1])/100 -
x.ax, par("usr")[4] - (par("usr")[4] - par("usr")[3])/100,
legend = filenames, lty = 1, lwd = 2, col = cl)
}
else {
if (is(dat, "ExpressionSet"))
plotDensity(as.matrix(exprs(dat)), lty = cl, lwd = 2, col = 1:length(filenames), main=title)
x.ax <- legend(1, 1, legend = filenames, lty = 1, lwd = 2,
col = cl, plot = FALSE)$rect$w
y.ax <- legend(1, 1, legend = filenames, lty = 1, lwd = 2,
col = cl, plot = FALSE)$rect$h
ydiff <- par("usr")[4] - par("usr")[3]
if (y.ax < ydiff) {
legend(par("usr")[2] - (par("usr")[2] - par("usr")[1])/100 -
x.ax, par("usr")[4] - (par("usr")[4] - par("usr")[3])/100,
legend = filenames, lty = cl, lwd = 2, col = 1:length(filenames))
}
else {
cexval <- 1
while (y.ax > ydiff) {
cexval <- cexval - 0.05
y.ax <- legend(1, 1, legend = filenames, lty = 1,
lwd = 2, col = cl, plot = FALSE, cex = cexval)$rect$h
x.ax <- legend(1, 1, legend = filenames, lty = 1,
lwd = 2, col = cl, plot = FALSE, cex = cexval)$rect$w
}
legend(par("usr")[2] - (par("usr")[2] - par("usr")[1])/100 -
x.ax, par("usr")[4] - (par("usr")[4] - par("usr")[3])/100,
legend = filenames, lty = cl, lwd = 2, col = 1:length(filenames),
cex = cexval)
}
}
}
make.cl <- function(filenames){
## A function to make a classlabel for plotting
## Check for number of files
if(length(filenames) <= 8)
cl <- 1 : length(filenames)
if(length(filenames) > 8){
mod <- floor(length(filenames)/8)
cl <- NULL
for(i in 1 : mod){
cl <- c(cl, rep(i, 8))
}
rem <- length(filenames) - mod*8
cl <- c(cl, rep(mod + 1, rem))
}
cl
}
if(affylmGUIenvironment$exonAffyData.Available){
##makning the menu for selecting gene or exon level density plot
Try(ttGeneExonMethod <- tktoplevel(.affylmGUIglobals$ttMain))
Try(tkwm.deiconify(ttGeneExonMethod))
Try(tkgrab.set(ttGeneExonMethod))
Try(tkfocus(ttGeneExonMethod))
Try(tkwm.title(ttGeneExonMethod,"Gene/Exon level plots"))
Try(tkgrid(tklabel(ttGeneExonMethod,text=" ")))
Try(ttGeneExonMethodTcl <- tclVar("gene"))
Try(rbGene <- tkradiobutton(ttGeneExonMethod,text="Gene levels",variable=ttGeneExonMethodTcl,value="gene",font=.affylmGUIglobals$affylmGUIfont2))
Try(rbExon<-tkradiobutton(ttGeneExonMethod,text="Exon levels",variable=ttGeneExonMethodTcl,value="exon",font=.affylmGUIglobals$affylmGUIfont2))
Try(tkgrid(tklabel(ttGeneExonMethod,text=" "),rbGene))
Try(tkgrid(tklabel(ttGeneExonMethod,text=" "),rbExon))
Try(tkgrid.configure(rbGene,rbExon,columnspan=2,sticky="w"))
Try(tkgrid(tklabel(ttGeneExonMethod,text=" "),tklabel(ttGeneExonMethod,text=" ")))
Try(ReturnVal <- "")
Try(onCancel <- function() {Try(ReturnVal <<- "");Try(tkgrab.release(ttGeneExonMethod));Try(tkdestroy(ttGeneExonMethod));Try(tkfocus(.affylmGUIglobals$ttMain))})
Try(onOK <- function() {Try(ReturnVal <<- tclvalue(ttGeneExonMethodTcl));Try(tkgrab.release(ttGeneExonMethod));Try(tkdestroy(ttGeneExonMethod));Try(tkfocus(.affylmGUIglobals$ttMain))})
Try(OK.but <- tkbutton(ttGeneExonMethod,text="OK",command=onOK,font=.affylmGUIglobals$affylmGUIfont2))
Try(Cancel.but <- tkbutton(ttGeneExonMethod,text="Cancel",command=onCancel,font=.affylmGUIglobals$affylmGUIfont2))
Try(tkgrid(tklabel(ttGeneExonMethod,text=" "),OK.but,Cancel.but,tklabel(ttGeneExonMethod,text=" ")))
Try(tkgrid.configure(OK.but,sticky="e"))
Try(tkgrid.configure(Cancel.but,sticky="w"))
Try(tkgrid(tklabel(ttGeneExonMethod,text=" ")))
Try(tkbind(ttGeneExonMethod,"<Destroy>",function() {ReturnVal <- "";Try(tkgrab.release(ttGeneExonMethod));Try(tkfocus(.affylmGUIglobals$ttMain));}))
Try(tkbind(OK.but, "<Return>",onOK))
Try(tkbind(Cancel.but, "<Return>",onCancel))
Try(tkwait.window(ttGeneExonMethod))
if(ReturnVal=="gene"){
Try(NormalizedAffyData <- get("NormalizedAffyData",envir=affylmGUIenvironment))
plotHist(NormalizedAffyData, title="Gene level density plot")
} else if (ReturnVal=="exon") {
Try(exonAffyData <- get("exonAffyData",envir=affylmGUIenvironment))
plotHist(exonAffyData, title="Exon level density plot")
} else {
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="arrow"))
Try(return())
}
}
else{
Try(tkmessageBox(title="Gene/Exon level Histograms",message="No exon data are available! These data seem not to be exon arrays data",type="ok",icon="error"))
}
Try(tkmessageBox(title="Gene/Exon level Histograms",message=paste("Plots will be displayed in the main R window")))
}
################################################################################
#part of the functions used to evaluate sample size and statistical power estimation
# sd distribution
"sample.size.evaluation" <- function(){
# require(multtest) || stop("library multtest could not be found !")
# require(ssize) || stop("library ssize could not be found !")
#error if no data are loaded
Try(whichArrayPlatform <- get("whichArrayPlatform",envir=affylmGUIenvironment))
if(whichArrayPlatform ==""){
Try(tkmessageBox(title="Study design",message="No arrays have been loaded. Please try New or Open from the File menu.",type="ok",icon="error"))
Try(tkfocus(.affylmGUIglobals$ttMain))
Try(return())
}
#########################
if(whichArrayPlatform =="EXON"){
Try(NormalizedAffyData <- get("NormalizedAffyData", env=affylmGUIenvironment))
}else{
if(affylmGUIenvironment$NormalizedAffyData.Available){
Try(NormalizedAffyData <- get("NormalizedAffyData", env=affylmGUIenvironment))
} else {
Try(tkmessageBox(title="Sample size & Power plots",message="Normalized data are not available.\n Please calculate the probe set expression summaries ", type="ok", icon="error"))
Try(return())
}
}
Try(expression.values <- exprs(NormalizedAffyData))
#assigning fold.change graphical menu
Try(ttGetFC<-tktoplevel(.affylmGUIglobals$ttMain))
Try(tkwm.deiconify(ttGetFC))
Try(tkgrab.set(ttGetFC))
Try(tkfocus(ttGetFC))
Try(tkwm.title(ttGetFC,"Assigning Fold Change"))
Try(tkgrid(tklabel(ttGetFC,text=" ")))
Try(FCnum <- "")
Try(Local.FC <- tclVar(init=FCnum))
Try(entry.FC <-tkentry(ttGetFC,width="3",font=.affylmGUIglobals$affylmGUIfont2,textvariable=Local.FC,bg="white"))
Try(tkgrid(tklabel(ttGetFC,text="Please Fold Change value.",font=.affylmGUIglobals$affylmGUIfont2)))
Try(tkgrid(entry.FC))
onOK <- function()
{
Try(FCnum <- as.numeric(tclvalue(Local.FC)))
if(nchar(FCnum)==0)
FCnum <- "Unselected"
Try(assign("FCnum",FCnum,affylmGUIenvironment))
Try(tclvalue(.affylmGUIglobals$FCTcl) <- FCnum)
Try(tkgrab.release(ttGetFC));Try(tkdestroy(ttGetFC));Try(tkfocus(.affylmGUIglobals$ttMain))
}
Try(OK.but <-tkbutton(ttGetFC,text=" OK ",command=onOK,font=.affylmGUIglobals$affylmGUIfont2))
Try(tkgrid(tklabel(ttGetFC,text=" ")))
Try(tkgrid(OK.but))
Try(tkgrid.configure(OK.but))
Try(tkgrid(tklabel(ttGetFC,text=" ")))
Try(tkfocus(entry.FC))
Try(tkbind(entry.FC, "<Return>",onOK))
Try(tkbind(ttGetFC, "<Destroy>", function(){Try(tkgrab.release(ttGetFC));Try(tkfocus(.affylmGUIglobals$ttMain));return(0)}))
Try(tkwait.window(ttGetFC))
Try(tkfocus(.affylmGUIglobals$ttMain))
if(FCnum == "Unselected"){
Try(tkmessageBox(title="Sample size & Power plots",message="Fold change threshold was not selected.\nAborting analysis.", type="ok", icon="error"))
Try(return())
}
#######################################################Ã Ã
#assigning power and sig.level grphical menu
Try(ttGetPower<-tktoplevel(.affylmGUIglobals$ttMain))
Try(tkwm.deiconify(ttGetPower))
Try(tkgrab.set(ttGetPower))
Try(tkfocus(ttGetPower))
Try(tkwm.title(ttGetPower,"Assigning the Statistical Power"))
Try(tkgrid(tklabel(ttGetPower,text=" ")))
Try(Powernum <- "")
Try(Local.Power <- tclVar(init=Powernum))
Try(entry.Power <-tkentry(ttGetPower,width="3",font=.affylmGUIglobals$affylmGUIfont2,textvariable=Local.Power,bg="white"))
Try(tkgrid(tklabel(ttGetPower,text="Please assign a Power value, \ni.e. any value between 0 and 1",font=.affylmGUIglobals$affylmGUIfont2)))
Try(tkgrid(entry.Power))
onOK <- function()
{
Try(Powernum <- as.numeric(tclvalue(Local.Power)))
if(nchar(Powernum)==0)
Powernum <- "Unselected"
Try(assign("Powernum",Powernum,affylmGUIenvironment))
Try(tclvalue(.affylmGUIglobals$PowerTcl) <- Powernum)
Try(tkgrab.release(ttGetPower));Try(tkdestroy(ttGetPower));Try(tkfocus(.affylmGUIglobals$ttMain))
}
Try(OK.but <-tkbutton(ttGetPower,text=" OK ",command=onOK,font=.affylmGUIglobals$affylmGUIfont2))
Try(tkgrid(tklabel(ttGetPower,text=" ")))
Try(tkgrid(OK.but))
Try(tkgrid.configure(OK.but))
Try(tkgrid(tklabel(ttGetPower,text=" ")))
Try(tkfocus(entry.Power))
Try(tkbind(entry.Power, "<Return>",onOK))
Try(tkbind(ttGetPower, "<Destroy>", function(){Try(tkgrab.release(ttGetPower));Try(tkfocus(.affylmGUIglobals$ttMain));return(0)}))
Try(tkwait.window(ttGetPower))
Try(tkfocus(.affylmGUIglobals$ttMain))
if(Powernum == "Unselected"){
Try(tkmessageBox(title="Sample size & Power plots",message="Power threshold was not selected.\nAborting analysis.", type="ok", icon="error"))
Try(return())
}
#######################################################Ã Ã
#######################################################Ã Ã
#assigning power and sig.level grphical menu
Try(ttGetSL<-tktoplevel(.affylmGUIglobals$ttMain))
Try(tkwm.deiconify(ttGetSL))
Try(tkgrab.set(ttGetSL))
Try(tkfocus(ttGetSL))
Try(tkwm.title(ttGetSL,"Assigning the significance level"))
Try(tkgrid(tklabel(ttGetSL,text=" ")))
Try(SLnum <- "")
Try(Local.SL <- tclVar(init=SLnum))
Try(entry.SL <-tkentry(ttGetSL,width="4",font=.affylmGUIglobals$affylmGUIfont2,textvariable=Local.SL,bg="white"))
Try(tkgrid(tklabel(ttGetSL,text="Please assign the significance level, \n, i.e. 0.05 or lower",font=.affylmGUIglobals$affylmGUIfont2)))
Try(tkgrid(entry.SL))
onOK <- function()
{
Try(SLnum <- as.numeric(tclvalue(Local.SL)))
if(nchar(SLnum)==0)
SLnum <- "Unselected"
Try(assign("SLnum",SLnum,affylmGUIenvironment))
Try(tclvalue(.affylmGUIglobals$SLTcl) <- SLnum)
Try(tkgrab.release(ttGetSL));Try(tkdestroy(ttGetSL));Try(tkfocus(.affylmGUIglobals$ttMain))
}
Try(OK.but <-tkbutton(ttGetSL,text=" OK ",command=onOK,font=.affylmGUIglobals$affylmGUIfont2))
Try(tkgrid(tklabel(ttGetSL,text=" ")))
Try(tkgrid(OK.but))
Try(tkgrid.configure(OK.but))
Try(tkgrid(tklabel(ttGetSL,text=" ")))
Try(tkfocus(entry.SL))
Try(tkbind(entry.SL, "<Return>",onOK))
Try(tkbind(ttGetSL, "<Destroy>", function(){Try(tkgrab.release(ttGetSL));Try(tkfocus(.affylmGUIglobals$ttMain));return(0)}))
Try(tkwait.window(ttGetSL))
Try(tkfocus(.affylmGUIglobals$ttMain))
if(SLnum == "Unselected"){
Try(tkmessageBox(title="Sample size & Power plots",message="Significance threshold was not selected.\nAborting analysis.", type="ok", icon="error"))
Try(return())
}
#######################################################Ã Ã
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="watch"))
Try(common.sd<-function(x){
covariate.data <<- affylmGUIenvironment$Targets$Target
target.unique <- unique(covariate.data)
common.sd1<- sqrt((sd(x[which(covariate.data==target.unique[1])])^2*(length(which(covariate.data==target.unique[1]))-1))
+(sd(x[which(covariate.data==target.unique[2])])^2*(length(which(covariate.data==target.unique[2]))-1))/
(length(which(covariate.data==target.unique[1]))+length(which(covariate.data==target.unique[2]))-2))
})#Wei et al. BMC Genomics. 2004, 5:87
Try(exp.sd <- apply(expression.values, 1, common.sd))
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="arrow"))
########################################################
#defining if ssize or delta function to be used
##makning the menu for selecting IQR threshold
Try(ttGetPlotMethod <- tktoplevel(.affylmGUIglobals$ttMain))
Try(tkwm.deiconify(ttGetPlotMethod))
Try(tkgrab.set(ttGetPlotMethod))
Try(tkfocus(ttGetPlotMethod))
Try(tkwm.title(ttGetPlotMethod,"Sample size or Power plot"))
Try(tkgrid(tklabel(ttGetPlotMethod,text=" ")))
Try(ttGetPlotMethodTcl <- tclVar("delta"))
Try(rbSsize <- tkradiobutton(ttGetPlotMethod,text="Sample size plot",variable=ttGetPlotMethodTcl,value="ssize",font=.affylmGUIglobals$affylmGUIfont2))
Try(rbDelta<-tkradiobutton(ttGetPlotMethod,text="Power plot",variable=ttGetPlotMethodTcl,value="delta",font=.affylmGUIglobals$affylmGUIfont2))
Try(tkgrid(tklabel(ttGetPlotMethod,text=" "),rbSsize))
Try(tkgrid(tklabel(ttGetPlotMethod,text=" "),rbDelta))
Try(tkgrid.configure(rbSsize,rbDelta,columnspan=2,sticky="w"))
Try(tkgrid(tklabel(ttGetPlotMethod,text=" "),tklabel(ttGetPlotMethod,text=" ")))
Try(ReturnVal <- "")
Try(onCancel <- function() {Try(ReturnVal <<- "");Try(tkgrab.release(ttGetPlotMethod));Try(tkdestroy(ttGetPlotMethod));Try(tkfocus(.affylmGUIglobals$ttMain))})
Try(onOK <- function() {Try(ReturnVal <<- tclvalue(ttGetPlotMethodTcl));Try(tkgrab.release(ttGetPlotMethod));Try(tkdestroy(ttGetPlotMethod));Try(tkfocus(.affylmGUIglobals$ttMain))})
Try(OK.but <- tkbutton(ttGetPlotMethod,text="OK",command=onOK,font=.affylmGUIglobals$affylmGUIfont2))
Try(Cancel.but <- tkbutton(ttGetPlotMethod,text="Cancel",command=onCancel,font=.affylmGUIglobals$affylmGUIfont2))
Try(tkgrid(tklabel(ttGetPlotMethod,text=" "),OK.but,Cancel.but,tklabel(ttGetPlotMethod,text=" ")))
Try(tkgrid.configure(OK.but,sticky="e"))
Try(tkgrid.configure(Cancel.but,sticky="w"))
Try(tkgrid(tklabel(ttGetPlotMethod,text=" ")))
Try(tkbind(ttGetPlotMethod,"<Destroy>",function() {ReturnVal <- "";Try(tkgrab.release(ttGetPlotMethod));Try(tkfocus(.affylmGUIglobals$ttMain));}))
Try(tkbind(OK.but, "<Return>",onOK))
Try(tkbind(Cancel.but, "<Return>",onCancel))
Try(tkwait.window(ttGetPlotMethod))
if(ReturnVal <- ""){
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="arrow"))
Try(return())
}
#################################################################################
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="watch"))
Try(fold.change <- get("FCnum", env=affylmGUIenvironment))
Try(power <- get("Powernum", env=affylmGUIenvironment))
Try(sig.level <- get("SLnum", env=affylmGUIenvironment))
#defining the significance threshold using BH correction
Try(covariate.data <- affylmGUIenvironment$Targets$Target)
Try(target.unique <- unique(covariate.data))
if((length(which(covariate.data==target.unique[1])) + length(which(covariate.data==target.unique[2]))) == length(covariate.data)){
Try(covariate.data[which(covariate.data==target.unique[1])] <- 0)
Try(covariate.data[which(covariate.data==target.unique[2])]<- 1)
Try(covariate.data <- as.numeric(covariate.data))
Try(teststat <- mt.teststat(expression.values, covariate.data))
Try(rawp0 <- 2 * (1 - pnorm(abs(teststat))))
Try(res <- mt.rawp2adjp(rawp0, "BH"))
Try(adjp <- res$adjp)
Try(sig.level.BH <- max(adjp[which(adjp[,2] <= sig.level),1]))
####################################################################################
#pow, power.plot compute and display a cumulative plot of the fraction of
#genes achieving a specified power for a fixed sample size (n), effect size
#(delta), and significance level (sig.level).
#Try(all.power <- pow(sd = exp.sd, n = length(covariate.data), delta = log2(fold.change), sig.level = sig.level))
#Try( power.plot(all.power, lwd = 2, col = "blue")
# xmax <- par("usr")[2] - 0.05
# ymax <- par("usr")[4] - 0.05
# legend(x = xmax, y = ymax, legend = strsplit(paste("n=", n, ",","fold change=", fold.change, ",", "alpha=", sig.level, ",", "# genes=", nobs(exp.sd), sep = ""), ",")[[1]], xjust = 1, yjust = 1, cex = 1)
#)
#ssize,ssize.plot compute and display a cumulative plot of the fraction of
#genes for which a specified sample size is sufficient to achieve a specified
#power (power), effect size (delta), and significance level (sig.level).
if(ReturnVal == "ssize"){
Try(all.size <- ssize(sd = exp.sd, delta = log2(fold.change), sig.level = sig.level.BH, power = power, alpha.correct="") )
Try( ssize.plot(all.size, lwd = 2, col = "magenta", xlim = c(1, 20)))
Try( xmax <- par("usr")[2] - 1)
Try( ymin <- par("usr")[3] + 0.05 )
Try( legend(x = xmax, y = ymin, legend = strsplit(paste("fold change=", fold.change, ",", "alpha=", sig.level, ",", "power=", power, ",", "# genes=", nobs(exp.sd), sep = ""), ",")[[1]], xjust = 1, yjust = 0, cex = 1) )
Try( title(paste("Sample Size to Detect ", fold.change,"-Fold Change", collapse="")))
Try(tkmessageBox(title="Sample size plot",message="Plot is shown in the main R window", type="ok", icon="info"))
} else{
#delta,delta.plot compute and display a cumulative plot of the fraction of
#genes which can achieve a specified power (power), for a specified sample
#size (n), and significance level (sig.level) for a range of effect
#sizes.
Try(all.delta <- delta(sd = exp.sd, power = power, n = length(covariate.data)/2, sig.level = sig.level.BH, alpha.correct=""))
Try( .delta.plot1(all.delta, lwd = 2, col = "magenta", xlim = c(1, 10)) )
Try( xmax <- par("usr")[2] - 1 )
Try( ymin <- par("usr")[3] + 0.05)
Try( legend(x = xmax, y = ymin, legend = strsplit(paste("n=", length(covariate.data)/2, ",", "alpha=", sig.level, ",", "power=", power, ",", "# genes=", nobs(exp.sd), sep = ""), ",")[[1]], xjust = 1, yjust = 0, cex = 1))
Try( title(paste("Fold Change to Achieve", power * 100, "% Power", collapse=" ")))
Try(tkmessageBox(title="Power plot",message="Plot is shown in the main R window", type="ok", icon="info"))
}
} else Try(tkmessageBox(title="Sample size & Power plots",message="This analysis can be applied only to 2 group experiment\nReorganize your data to fullfil these requirements", type="ok", icon="error"))
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="arrow"))
}
#internal because siggenes overlay this function
.delta.plot1 <- function(x,
xlab="Fold Change",
ylab="Proportion of Genes",
marks=c(1.5, 2.0, 2.5, 3.0, 4.0, 6.0,10),
...)
{
n <- nobs(x)
inv <- list()
inv$x <- sort(x)
inv$y <- ecdf(x)(inv$x)
plot(inv, type="s",
xlab=xlab, ylab=ylab, yaxt="n",
..., )
vals <- pretty(inv$y * n)
labels <- paste( format(vals/n*100,digits=2), "%=", vals, sep='')
axis(side=2, at=vals/n, labels=labels, srt=90, adj=0.5)
if(!is.null(marks) && length(marks)>0 )
{
xmin <- par("usr")[1]
ymin <- par("usr")[3]
for(mark in marks)
{
y <- inv$y[ which(inv$x>mark)[1]-1 ]
lines( x=rbind( c(mark, ymin),
c(mark, y) ),
lty=2, col='red' )
text( x=mark, y=ymin, label=format(mark,2), col="red", adj=c(0,0))
lines( x=rbind( c(xmin, y),
c(mark, y) ),
lty=2, col='red' )
text( x=xmin, y=y,
label=paste(format(y*100,digits=2),"%=",
format(y*n,digits=2), sep=''),
col="red", adj=c(0,0), xpd=TRUE)
}
}
}
################################################################################
#part of the functions used to evaluate sample size and statistical power estimation sizepower package
# sd distribution
"sample.size.evaluation1" <- function(){
# require(sizepower) || stop("library sizepower could not be found !")
#error if no data are loaded
Try(whichArrayPlatform <- get("whichArrayPlatform",envir=affylmGUIenvironment))
if(whichArrayPlatform ==""){
Try(tkmessageBox(title="Study design",message="No arrays have been loaded. Please try New or Open from the File menu.",type="ok",icon="error"))
Try(tkfocus(.affylmGUIglobals$ttMain))
Try(return())
}
#########################
if(whichArrayPlatform =="EXON"){
Try(NormalizedAffyData <- get("NormalizedAffyData", env=affylmGUIenvironment))
}else{
if(affylmGUIenvironment$NormalizedAffyData.Available){
Try(NormalizedAffyData <- get("NormalizedAffyData", env=affylmGUIenvironment))
} else {
Try(tkmessageBox(title="Sample size & Power Experiment Estimation",message="Normalized data are not available.\n Please calculate the probe set expression summaries ", type="ok", icon="error"))
Try(return())
}
}
Try(expression.values <- exprs(NormalizedAffyData))
covariate.data <- affylmGUIenvironment$Targets$Target
target.unique <- unique(covariate.data)
if(length(target.unique)>2){
Try(tkmessageBox(title="Sample size & Power Experiment Estimation",message="This function apply only two class experiment.", type="ok", icon="error"))
return()
} else{
##Selecting the function to be used
Try(ttsizepowerMethod <- tktoplevel(.affylmGUIglobals$ttMain))
Try(tkwm.deiconify(ttsizepowerMethod))
Try(tkgrab.set(ttsizepowerMethod))
Try(tkfocus(ttsizepowerMethod))
Try(tkwm.title(ttsizepowerMethod,"Sample size & Power Experiment Estimation"))
Try(tkgrid(tklabel(ttsizepowerMethod,text=" ")))
Try(ttsizepowerMethodTcl <- tclVar("size"))
Try(rbSsize <- tkradiobutton(ttsizepowerMethod,text="Sample size estimation",variable=ttsizepowerMethodTcl,value="size",font=.affylmGUIglobals$affylmGUIfont2))
Try(rbPower<-tkradiobutton(ttsizepowerMethod,text="Power estimation",variable=ttsizepowerMethodTcl,value="power",font=.affylmGUIglobals$affylmGUIfont2))
Try(tkgrid(tklabel(ttsizepowerMethod,text=" "),rbSsize))
Try(tkgrid(tklabel(ttsizepowerMethod,text=" "),rbPower))
Try(tkgrid.configure(rbSsize,rbPower,columnspan=2,sticky="w"))
Try(tkgrid(tklabel(ttsizepowerMethod,text=" "),tklabel(ttsizepowerMethod,text=" ")))
Try(ReturnVal <- "")
Try(onCancel <- function() {Try(ReturnVal <<- "");Try(tkgrab.release(ttsizepowerMethod));Try(tkdestroy(ttsizepowerMethod));Try(tkfocus(.affylmGUIglobals$ttMain))})
Try(onOK <- function() {Try(ReturnVal <<- tclvalue(ttsizepowerMethodTcl));Try(tkgrab.release(ttsizepowerMethod));Try(tkdestroy(ttsizepowerMethod));Try(tkfocus(.affylmGUIglobals$ttMain))})
Try(OK.but <- tkbutton(ttsizepowerMethod,text="OK",command=onOK,font=.affylmGUIglobals$affylmGUIfont2))
Try(Cancel.but <- tkbutton(ttsizepowerMethod,text="Cancel",command=onCancel,font=.affylmGUIglobals$affylmGUIfont2))
Try(tkgrid(tklabel(ttsizepowerMethod,text=" "),OK.but,Cancel.but,tklabel(ttsizepowerMethod,text=" ")))
Try(tkgrid.configure(OK.but,sticky="e"))
Try(tkgrid.configure(Cancel.but,sticky="w"))
Try(tkgrid(tklabel(ttsizepowerMethod,text=" ")))
Try(tkbind(ttsizepowerMethod,"<Destroy>",function() {ReturnVal <- "";Try(tkgrab.release(ttsizepowerMethod));Try(tkfocus(.affylmGUIglobals$ttMain));}))
Try(tkbind(OK.but, "<Return>",onOK))
Try(tkbind(Cancel.but, "<Return>",onCancel))
Try(tkwait.window(ttsizepowerMethod))
#######################################################Ã Ã
if(ReturnVal == ""){
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="arrow"))
Try(return())
}
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="watch"))
Try(common.sd<-function(x){
covariate.data <<- affylmGUIenvironment$Targets$Target
target.unique <- unique(covariate.data)
common.sd1<- sqrt((sd(x[which(covariate.data==target.unique[1])])^2*(length(which(covariate.data==target.unique[1]))-1))
+(sd(x[which(covariate.data==target.unique[2])])^2*(length(which(covariate.data==target.unique[2]))-1))/
(length(which(covariate.data==target.unique[1]))+length(which(covariate.data==target.unique[2]))-2))
})#Wei et al. BMC Genomics. 2004, 5:87
Try(exp.sd <- apply(expression.values, 1, common.sd))
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="arrow"))
########################################################
Try(if(ReturnVal=="size"){
# Try(tkmessageBox(title="Sample sixe evaluation",message="This routine computes the required sample size.",type="ok",icon="info"))
##making the menu for selecting sample sixe parameters
Try(ttsizepowerDialog<-tktoplevel(.affylmGUIglobals$ttMain))
Try(tkwm.deiconify(ttsizepowerDialog))
Try(tkgrab.set(ttsizepowerDialog))
Try(tkfocus(ttsizepowerDialog))
Try(tkwm.title(ttsizepowerDialog,"Sample size parameters"))
Try(tkgrid(tklabel(ttsizepowerDialog,text=" ")))
#Try(frame1 <- tkframe(ttsizepowerDialog,relief="groove",borderwidth=2))
#Try(HowManyQuestion1 <- tklabel(frame1,text="Mean number of false positives",font=.affylmGUIglobals$affylmGUIfont2))
#Try(tkgrid(HowManyQuestion1))
#Try(tkgrid.configure(HowManyQuestion1,columnspan=2,sticky="w"))
Try(fTcl <- tclVar("1"))
#Try(f1.but <- tkradiobutton(frame1,text="1",variable=fTcl,value=1,font=.affylmGUIglobals$affylmGUIfont2))
#Try(f2.but <- tkradiobutton(frame1,text="5",variable=fTcl,value=5,font=.affylmGUIglobals$affylmGUIfont2))
#Try(f3.but <- tkradiobutton(frame1,text="10",variable=fTcl,value=10,font=.affylmGUIglobals$affylmGUIfont2))
#Try(f4.but <- tkradiobutton(frame1,text="20",variable=fTcl,value=20,font=.affylmGUIglobals$affylmGUIfont2))
#Try(f5.but <- tkradiobutton(frame1,text="40",variable=fTcl,value=40,font=.affylmGUIglobals$affylmGUIfont2))
#Try(tkgrid(f1.but,sticky="w"))
#Try(tkgrid(f2.but,sticky="w"))
#Try(tkgrid(f3.but,sticky="w"))
#Try(tkgrid(f4.but,sticky="w"))
#Try(tkgrid(f5.but,sticky="w"))
#Try(tkgrid.configure(HowManyQuestion1,f1.but,f2.but,f3.but,f4.but,f5.but,sticky="w"))
Try(frame2 <- tkframe(ttsizepowerDialog,relief="groove",borderwidth=2))
Try(powerLabel <- tklabel(frame2,text="Power level for an individual gene",font=.affylmGUIglobals$affylmGUIfont2))
Try(tkgrid(powerLabel,sticky="w"))
Try(tkgrid.configure(powerLabel,sticky="w"))
Try(powerTcl <- tclVar("0.9"))
Try(p1.but <- tkradiobutton(frame2,text="0.99",variable=powerTcl,value=0.99,font=.affylmGUIglobals$affylmGUIfont2))
Try(p2.but <- tkradiobutton(frame2,text="0.95",variable=powerTcl,value=0.95,font=.affylmGUIglobals$affylmGUIfont2))
Try(p3.but <- tkradiobutton(frame2,text="0.9",variable=powerTcl,value=0.9,font=.affylmGUIglobals$affylmGUIfont2))
Try(p4.but <- tkradiobutton(frame2,text="0.85",variable=powerTcl,value=0.85,font=.affylmGUIglobals$affylmGUIfont2))
Try(p5.but <- tkradiobutton(frame2,text="0.8",variable=powerTcl,value=0.8,font=.affylmGUIglobals$affylmGUIfont2))
Try(tkgrid(p1.but,sticky="w"))
Try(tkgrid(p2.but,sticky="w"))
Try(tkgrid(p3.but,sticky="w"))
Try(tkgrid(p4.but,sticky="w"))
Try(tkgrid(p5.but,sticky="w"))
Try(frame3 <- tkframe(ttsizepowerDialog,relief="groove",borderwidth=2))
Try(fcLabel <- tklabel(frame3,text="Absolute log2(Fold Change)",font=.affylmGUIglobals$affylmGUIfont2))
Try(tkgrid(fcLabel,sticky="w"))
Try(tkgrid.configure(fcLabel,sticky="w"))
Try(fcTcl <- tclVar("1"))
Try(fc1.but <- tkradiobutton(frame3,text="1",variable=fcTcl,value=1,font=.affylmGUIglobals$affylmGUIfont2))
Try(fc2.but <- tkradiobutton(frame3,text="1.5" ,variable=fcTcl,value=1.5 ,font=.affylmGUIglobals$affylmGUIfont2))
Try(fc3.but <- tkradiobutton(frame3,text="2" ,variable=fcTcl,value=2 ,font=.affylmGUIglobals$affylmGUIfont2))
Try(fc4.but <- tkradiobutton(frame3,text="2.5",variable=fcTcl,value=2.5,font=.affylmGUIglobals$affylmGUIfont2))
Try(tkgrid(fc1.but,sticky="w"))
Try(tkgrid(fc2.but ,sticky="w"))
Try(tkgrid(fc3.but ,sticky="w"))
Try(tkgrid(fc4.but,sticky="w"))
Try(Abort <- 1)
sizepower.param <- list()
Try(onOK <- function()
{
Try(sizepower.param[[1]] <<- tclvalue(fTcl))
Try(tkgrab.release(ttsizepowerDialog))
Try(tkdestroy(ttsizepowerDialog))
Try(tkfocus(.affylmGUIglobals$ttMain))
Try(sizepower.param[[2]] <<- tclvalue(powerTcl))
Try(sizepower.param[[3]] <<- tclvalue(fcTcl))
Try(Abort <<- 0)
})
#Try(onHelp <- function() Try(help("topTable",htmlhelp=TRUE)))
Try(frame4 <- tkframe(ttsizepowerDialog,borderwidth=2))
Try(onCancel <- function() {Try(tkgrab.release(ttsizepowerDialog));Try(tkdestroy(ttsizepowerDialog));Try(tkfocus(.affylmGUIglobals$ttMain));Abort <<- 1})
Try(OK.but <-tkbutton(frame4,text=" OK ",command=onOK,font=.affylmGUIglobals$affylmGUIfont2))
Try(Cancel.but <-tkbutton(frame4,text=" Cancel ",command=onCancel,font=.affylmGUIglobals$affylmGUIfont2))
#Try(Help.but <-tkbutton(frame4,text=" Help ",command=onHelp,font=.affylmGUIglobals$affylmGUIfont2))
Try(tkgrid(tklabel(frame4,text=" "),OK.but,Cancel.but,tklabel(frame4,text=" ")))
Try(tkgrid(tklabel(ttsizepowerDialog,text=" "),frame2,tklabel(ttsizepowerDialog,text=" ")))
#Try(tkgrid(tklabel(ttsizepowerDialog,text=" ")))
Try(tkgrid(tklabel(ttsizepowerDialog,text=" "),frame3,frame4,tklabel(ttsizepowerDialog,text=" ")))
#Try(tkgrid(tklabel(ttsizepowerProDialog,text=" ")))
Try(tkgrid.configure(frame2, frame3,sticky="w"))
#Try(tkgrid.configure(frame1,frame3,sticky="w"))
# Try(tkgrid.configure(frame4,sticky="s"))
Try(tkfocus(ttsizepowerDialog))
Try(tkbind(ttsizepowerDialog, "<Destroy>", function() {Try(tkgrab.release(ttsizepowerDialog));Try(tkfocus(.affylmGUIglobals$ttMain));}))
Try(tkwait.window(ttsizepowerDialog))
Try(if(Abort==1) return())
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="watch"))
#In this case the sample size is based on the mean of the common variance
Try(mysample <- sampleSize.randomized(ER0 = as.numeric(sizepower.param[[1]]),
G0 = dim(expression.values)[1],
power = as.numeric(sizepower.param[[2]]),
absMu1 = as.numeric(sizepower.param[[3]]),
sigmad = sqrt(2)*mean(exp.sd))
)
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="arrow"))
Try(tkmessageBox(title="Sample size evaluation",message=paste("Given a",sizepower.param[[1]],"mean number of false positives\n",sizepower.param[[2]],"power\n",sizepower.param[[3]],"absolute mean difference in log-expression between treatment and control\n","The sample size (per group) is",mysample$n, sep=" "),type="ok",icon="info"))
Try(cat(paste("Sample size evaluation:\n","Given a",sizepower.param[[1]],"mean number of false positives\n",sizepower.param[[2]],"power\n",sizepower.param[[3]],"absolute mean difference in log-expression between treatment and control\n","The sample size (per group) is",mysample$n,"\n", sep=" ")))
} else {
# Try(tkmessageBox(title="Power evaluation",message="This routine computes the individual \npower value for a completely randomized design.\n This power value is the expected fraction of truly differentially expressed genes that \nwill be correctly declared as differentially expressed by the tests.",type="ok",icon="info"))
##making the menu for selecting the power parameters
Try(ttsizepowerDialog<-tktoplevel(.affylmGUIglobals$ttMain))
Try(tkwm.deiconify(ttsizepowerDialog))
Try(tkgrab.set(ttsizepowerDialog))
Try(tkfocus(ttsizepowerDialog))
Try(tkwm.title(ttsizepowerDialog,"Sample size parameters"))
Try(tkgrid(tklabel(ttsizepowerDialog,text=" ")))
#Try(frame1 <- tkframe(ttsizepowerDialog,relief="groove",borderwidth=2))
#Try(HowManyQuestion1 <- tklabel(frame1,text=
# "Mean number of false positives",font=.affylmGUIglobals$affylmGUIfont2))
#Try(tkgrid(HowManyQuestion1))
#Try(tkgrid.configure(HowManyQuestion1,columnspan=2,sticky="w"))
Try(fTcl <- tclVar("1"))
#Try(f1.but <- tkradiobutton(frame1,text="1",variable=fTcl,value=1,font=.affylmGUIglobals$affylmGUIfont2))
#Try(f2.but <- tkradiobutton(frame1,text="5",variable=fTcl,value=5,font=.affylmGUIglobals$affylmGUIfont2))
#Try(f3.but <- tkradiobutton(frame1,text="10",variable=fTcl,value=10,font=.affylmGUIglobals$affylmGUIfont2))
#Try(f4.but <- tkradiobutton(frame1,text="20",variable=fTcl,value=20,font=.affylmGUIglobals$affylmGUIfont2))
#Try(f5.but <- tkradiobutton(frame1,text="40",variable=fTcl,value=40,font=.affylmGUIglobals$affylmGUIfont2))
#Try(tkgrid(f1.but,sticky="w"))
#Try(tkgrid(f2.but,sticky="w"))
#Try(tkgrid(f3.but,sticky="w"))
#Try(tkgrid(f4.but,sticky="w"))
#Try(tkgrid(f5.but,sticky="w"))
#Try(tkgrid.configure(HowManyQuestion1,f1.but,f2.but,f3.but,f4.but,f5.but,sticky="w"))
Try(frame2 <- tkframe(ttsizepowerDialog,relief="groove",borderwidth=2))
Try(fcLabel <- tklabel(frame2,text="Absolute log2(Fold Change)",font=.affylmGUIglobals$affylmGUIfont2))
Try(tkgrid(fcLabel,sticky="w"))
Try(tkgrid.configure(fcLabel,sticky="w"))
Try(fcTcl <- tclVar("1"))
Try(fc1.but <- tkradiobutton(frame2,text="1",variable=fcTcl,value=1,font=.affylmGUIglobals$affylmGUIfont2))
Try(fc2.but <- tkradiobutton(frame2,text="1.5" ,variable=fcTcl,value=1.5 ,font=.affylmGUIglobals$affylmGUIfont2))
Try(fc3.but <- tkradiobutton(frame2,text="2" ,variable=fcTcl,value=2 ,font=.affylmGUIglobals$affylmGUIfont2))
Try(fc4.but <- tkradiobutton(frame2,text="2.5",variable=fcTcl,value=2.5,font=.affylmGUIglobals$affylmGUIfont2))
Try(tkgrid(fc1.but,sticky="w"))
Try(tkgrid(fc2.but ,sticky="w"))
Try(tkgrid(fc3.but ,sticky="w"))
Try(tkgrid(fc4.but,sticky="w"))
Try(Abort <- 1)
sizepower.param <- list()
Try(onOK <- function()
{
Try(sizepower.param[[1]] <<- tclvalue(fTcl))
Try(tkgrab.release(ttsizepowerDialog))
Try(tkdestroy(ttsizepowerDialog))
Try(tkfocus(.affylmGUIglobals$ttMain))
Try(sizepower.param[[2]] <<- tclvalue(fcTcl))
Try(Abort <<- 0)
})
#Try(onHelp <- function() Try(help("topTable",htmlhelp=TRUE)))
Try(frame3 <- tkframe(ttsizepowerDialog,borderwidth=2))
Try(onCancel <- function() {Try(tkgrab.release(ttsizepowerDialog));Try(tkdestroy(ttsizepowerDialog));Try(tkfocus(.affylmGUIglobals$ttMain));Abort <<- 1})
Try(OK.but <-tkbutton(frame3,text=" OK ",command=onOK,font=.affylmGUIglobals$affylmGUIfont2))
Try(Cancel.but <-tkbutton(frame3,text=" Cancel ",command=onCancel,font=.affylmGUIglobals$affylmGUIfont2))
#Try(Help.but <-tkbutton(frame4,text=" Help ",command=onHelp,font=.affylmGUIglobals$affylmGUIfont2))
Try(tkgrid(tklabel(frame3,text=" "),OK.but,Cancel.but,tklabel(frame3,text=" ")))
Try(tkgrid(tklabel(ttsizepowerDialog,text=" "),frame2,tklabel(ttsizepowerDialog,text=" ")))
#Try(tkgrid(tklabel(ttsizepowerDialog,text=" ")))
Try(tkgrid(tklabel(ttsizepowerDialog,text=" "),frame3,tklabel(ttsizepowerDialog,text=" ")))
#Try(tkgrid(tklabel(ttsizepowerProDialog,text=" ")))
Try(tkgrid.configure(frame2,frame3,sticky="w"))
# Try(tkgrid.configure(frame4,sticky="s"))
Try(tkfocus(ttsizepowerDialog))
Try(tkbind(ttsizepowerDialog, "<Destroy>", function() {Try(tkgrab.release(ttsizepowerDialog));Try(tkfocus(.affylmGUIglobals$ttMain));}))
Try(tkwait.window(ttsizepowerDialog))
Try(if(Abort==1) return())
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="watch"))
#In this case the sample size is based on the mean of the common variance
Try(mysample <- power.randomized(ER0 = as.numeric(sizepower.param[[1]]),
G0 = dim(expression.values)[1],
absMu1 = as.numeric(sizepower.param[[2]]),
sigmad = sqrt(2)*mean(exp.sd),
n=ceiling(dim(expression.values)[2]/2))
)
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="arrow"))
Try(tkmessageBox(title="Power evaluation",message=paste("Given a",sizepower.param[[1]],"mean number of false positives\n",(dim(expression.values)[2]/2),"replicates for each condition\n",sizepower.param[[2]]," absolute mean difference in log-expression between treatment and control\n","the power is",signif(mysample$power,2), sep=" "),type="ok",icon="info"))
Try(cat(paste("Power evaluation","Given a",sizepower.param[[1]],"mean number of false positives\n",(dim(expression.values)[2]/2),"replicates for each condition\n",sizepower.param[[2]]," absolute mean difference in log-expression between treatment and control\n","the power is",signif(mysample$power,2),"\n", sep=" ")))
})
}
}
################################################################################
PlotOptionsv1 <- function()
{
Try(ttGetPlotOptions<-tktoplevel(.affylmGUIglobals$ttMain))
Try(tkwm.title(ttGetPlotOptions,"Plot Options"))
Try(tkwm.deiconify(ttGetPlotOptions))
Try(tkgrab.set(ttGetPlotOptions))
Try(tkframe1 <- tkframe(ttGetPlotOptions,borderwidth=2))
Try(tkframe2 <- tkframe(tkframe1,relief="groove",borderwidth=2))
Try(tkframe4<-tkframe(tkframe1,borderwidth=2))
Try(tkgrid(tklabel(tkframe1,text=" ")))
Try(tkgrid(tklabel(tkframe2,text="Choose a graphics device for plotting.",font=.affylmGUIglobals$affylmGUIfont2),column=2,rowspan=1,columnspan=2,sticky="w"))
Try(affylmGUIglobals <- get(".affylmGUIglobals",envir=.GlobalEnv))
Try(if (!("graphicsDevice" %in% names(affylmGUIglobals)))
{
Try(affylmGUIglobals$graphicsDevice <- "R")
Try(assign(".affylmGUIglobals",affylmGUIglobals,.GlobalEnv))
})
#Try(graphicsDevice <- .affylmGUIglobals$graphicsDevice)
Try(graphicsDevice <- "R")
Try(graphicsDeviceTcl <- tclVar(graphicsDevice))
Try(tkrplot.but <- tkradiobutton(tkframe2,text="Tk R Plot",variable=graphicsDeviceTcl,value="tkrplot",font=.affylmGUIglobals$affylmGUIfont2))
Try(R.but <- tkradiobutton(tkframe2,text="R",variable=graphicsDeviceTcl,value="R",font=.affylmGUIglobals$affylmGUIfont2))
Try(tkgrid(tkrplot.but,column=2))
Try(tkgrid(R.but,column=2))
Try(tkgrid.configure(tkrplot.but,R.but,sticky="w"))
Try(tkgrid(tkframe2))
Try(newGraphicsDevice <- "")
onOK <- function()
{
Try(newGraphicsDevice<<-tclvalue(graphicsDeviceTcl))
Try(tkgrab.release(ttGetPlotOptions))
Try(tkdestroy(ttGetPlotOptions))
Try(if (newGraphicsDevice==graphicsDevice)
return())
Try(graphicsDevice <- newGraphicsDevice)
Try(if (graphicsDevice=="R" && .Platform$OS.type=="windows")
Try(tkmessageBox(title="R graphics device",
message="It is strongly recommended that you run R in SDI (Single Document Interface) mode when using the R graphics device",icon="warning")))
Try(affylmGUIglobals <- get(".affylmGUIglobals",envir=.GlobalEnv))
Try(affylmGUIglobals$graphicsDevice <- graphicsDevice)
Try(assign(".affylmGUIglobals",affylmGUIglobals,.GlobalEnv))
Try(tkfocus(.affylmGUIglobals$ttMain))
}
Try(OK.but <-tkbutton(tkframe4,text=" OK ",command=onOK,font=.affylmGUIglobals$affylmGUIfont2))
Try(Cancel.but <-tkbutton(tkframe4,text=" Cancel ",command=function(){Try(tkgrab.release(ttGetPlotOptions));Try(tkdestroy(ttGetPlotOptions));newGraphicsDevice<-"";Try(tkfocus(.affylmGUIglobals$ttMain))},font=.affylmGUIglobals$affylmGUIfont2))
Try(onHelp <- function() tkmessageBox(title="Plotting Device",
message="The R graphics is device can be resized more easily, but it may be inconvenient for Windows users running R in MDI mode.",
icon="info"))
Try(Help.but <- tkbutton(tkframe4,text=" Help ",command=function()Try(onHelp()),font=.affylmGUIglobals$affylmGUIfont2))
Try(tkgrid(tklabel(tkframe4,text=" ")))
Try(tkgrid(OK.but,Cancel.but,Help.but))
Try(tkgrid.configure(OK.but,sticky="e"))
Try(tkgrid.configure(Cancel.but,sticky="e"))
Try(tkgrid.configure(Help.but,sticky="e"))
Try(tkgrid(tklabel(tkframe4,text=" ")))
Try(tkgrid(tkframe4))
Try(tkgrid(tkframe1))
Try(tkfocus(OK.but))
Try(tkbind(ttGetPlotOptions, "<Return>",onOK))
Try(tkbind(ttGetPlotOptions, "<Destroy>", function() {Try(tkgrab.release(ttGetPlotOptions));Try(tkfocus(.affylmGUIglobals$ttMain))}))
Try(tkwait.window(ttGetPlotOptions))
Try(tkdestroy(ttGetPlotOptions))
# This return value below is not used. The function above is used for its effect
# on PlotOptions in affylmGUIenvironment
return(newGraphicsDevice)
}
################################################################################
affyPlotMA <- function(){
Try(ArraysLoaded <- get("ArraysLoaded", envir=affylmGUIenvironment))
Try(SlideNamesVec <- get("SlideNamesVec", envir=affylmGUIenvironment))
Try(RawAffyData <- get("RawAffyData",envir=affylmGUIenvironment))
Try(
if (ArraysLoaded==FALSE){
Try(tkmessageBox(title="M A Plot",message="Error: No arrays have been loaded.", icon="error",default="ok"))
return()
}
)
Try(LocalHScale <- .affylmGUIglobals$Myhscale)
Try(LocalVScale <- .affylmGUIglobals$Myvscale)
#
Try(SlideNums <- GetSlideNums())
Try(if (length(SlideNums)==0) return())
Try(slide1 <- SlideNums$slide1)
Try(slide2 <- SlideNums$slide2)
#
Try(WhetherToNormalize <- tclvalue(tkmessageBox(title="M A Plot",message="Use normalized data?",type="yesnocancel",icon="question")))
Try(if (WhetherToNormalize=="cancel") return())
#
Try(
if (WhetherToNormalize=="yes"){
Try(NormalizedAffyData.Available <- get("NormalizedAffyData.Available",envir=affylmGUIenvironment))
Try(
if (NormalizedAffyData.Available==FALSE){
NormalizeNow()
}
)
Try(NormalizedAffyData.Available <- get("NormalizedAffyData.Available",envir=affylmGUIenvironment))
Try(
if (NormalizedAffyData.Available==FALSE){
tkmessageBox(title="M A Plot",message="An error occured while trying to normalize the data.")
return()
}
)
Try(NormalizedAffyData <- get("NormalizedAffyData", envir=affylmGUIenvironment))
Try(NormalizedAffyData.exprs <- exprs(NormalizedAffyData))
Try(R <- NormalizedAffyData.exprs[,slide1]) # Using cDNA notation (R for one channel/array, G for the other)
Try(G <- NormalizedAffyData.exprs[,slide2]) # Using cDNA notation (R for one channel/array, G for the other)
pch <- 16
cex <- 0.2
}else{
Try(R <- log2(exprs(RawAffyData)[,slide1])) # Using cDNA notation (R for one channel/array, G for the other)
Try(G <- log2(exprs(RawAffyData)[,slide2])) # Using cDNA notation (R for one channel/array, G for the other)
pch <- "."
cex <- 1
}
)
# R and G are already log2ed.
M <- R - G
A <- 0.5*(R+G)
Try(
plotFunction <- function(){
Try(opar<-par(bg="white"))
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="watch"))
Try(plot(A,M,pch=pch,cex=cex,xlab=xLabel,ylab=yLabel))
Try(title(plotTitle))
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="arrow"))
Try(tmp<-par(opar))
}#end of plotFunction <- function()
)
Try(
if (WhetherToNormalize=="yes"){
Try(plotTitle<-paste("Normalized M A Plot (",SlideNamesVec[slide1]," vs ",SlideNamesVec[slide2],")",sep=""))
}else{
Try(plotTitle<-paste("Raw M A Plot (",SlideNamesVec[slide1]," vs ",SlideNamesVec[slide2],")",sep=""))
}
)
Try(plotLabels <- GetPlotLabels(plotTitle,"A","M"))
Try(if (length(plotLabels)==0) return())
Try(plotTitle <- plotLabels$plotTitle)
Try(xLabel <- plotLabels$xLabel)
Try(yLabel <- plotLabels$yLabel)
#
Try(
if(.affylmGUIglobals$graphicsDevice=="tkrplot"){
# require("tkrplot")
CopyToClip <- function() Try(tkrreplot(imgaffylmGUI))
Try(ttGraph<-tktoplevel(.affylmGUIglobals$ttMain))
Try(tkwm.withdraw(ttGraph))
Try(tkwm.title(ttGraph,plotTitle))
Try(imgaffylmGUI<-tkrplot(ttGraph,plotFunction,hscale=LocalHScale,vscale=LocalVScale))
Try(tkwm.title(ttGraph,plotTitle))
SetupPlotKeyBindings(tt=ttGraph,img=imgaffylmGUI)
SetupPlotMenus(tt=ttGraph,initialfile="",plotFunction,img=imgaffylmGUI)
Try(tkgrid(imgaffylmGUI))
Try(
if(as.numeric(tclvalue(tkwinfo("reqheight",imgaffylmGUI)))<10){ # Nothing plotted.
Try(tkdestroy(ttGraph))
}else{
Try(tkwm.deiconify(ttGraph))
Try(tkfocus(imgaffylmGUI))
}
)
}else{
Try(plot.new())
Try(plotFunction())
}
)
}#end of affyPlotMA <- function()
################################################################################
"rawBoxplotPN" <- function(){
#error if no data are loaded
Try(whichArrayPlatform <- get("whichArrayPlatform",envir=affylmGUIenvironment))
if(whichArrayPlatform ==""){
Try(tkmessageBox(title="QC",message="No arrays have been loaded. Please try New or Open from the File menu.",type="ok",icon="error"))
Try(tkfocus(.affylmGUIglobals$ttMain))
Try(return())
}
if(whichArrayPlatform!="EXON"){return()} #only on exons
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="watch"))
Try(localDir <- getwd())
Try(whichLib <- get("whichLib", affylmGUIenvironment))
Try(affylibs <- dir(system.file("affylibs",package="oneChannelGUI")))
Try(ctrl <- affylibs[intersect(grep(whichLib[[1]][1], affylibs), grep("controls", affylibs))])
#check if the affylibs are available else it install it
Try(if(length(ctrl) == 0){
tkmessageBox(title="QC",message="It seems that the Affymetrix/Apt libraries are not available.\nNext messages will help you to install/set them.",type="ok",icon="error")
aptFolder()
geneExonLibs()
})
Try(ctrl.table <- read.table(paste(system.file("affylibs",package="oneChannelGUI"),"/",ctrl, sep=""), sep="\t", as.is=T, header=T))
Try(pgf <- paste(system.file("affylibs",package="oneChannelGUI"),"/",affylibs[intersect(grep(whichLib[[1]][1], affylibs), grep("pgf", affylibs))],sep=""))
Try(clf <- paste(system.file("affylibs",package="oneChannelGUI"),"/",affylibs[intersect(grep(whichLib[[1]][1], affylibs), grep("clf", affylibs))],sep=""))
setwd(localDir)
Try(p.ctrl <- ctrl.table[which(ctrl.table[,2]=="pos_control"),])
Try(n.ctrl <- ctrl.table[which(ctrl.table[,2]=="neg_control"),])
Try(pn.ctrl <- rbind(p.ctrl, n.ctrl))
Try(write.table(pn.ctrl, "ctrlpn.txt", sep="\t", row.names=F))
#defining the temp file containing target info for apt extract
Try(Targets <- get("Targets",envir=affylmGUIenvironment))
Try(tempTarget <- tempfile(pattern = "target", tmpdir = getwd()))
Try(tempTarget <- sub( "\\\\","/",tempTarget)) #changing double backslach with slash
Try(write.table(Targets[,2:3], tempTarget, sep="\t", row.names =F, col.names = c("cel_files", "group_id")))
Try(tempOut <- tempfile(pattern = "out", tmpdir = getwd()))#creating a temp outfile
Try(tempOut <- sub( "\\\\","/",tempOut)) #changing double backslach with slash
#running apt-cel-extract
Try(extractCel <- paste(get("aptDir", affylmGUIenvironment),"/bin/apt-cel-extract", sep=""))
Try(extractCel <- paste(extractCel, " -o rawPN.txt ", "-p ", pgf ," -c ",clf," --probeset-ids ctrlpn.txt ", "--cel-files " , tempTarget, sep=""))
Try(cat("Be patient...... starting probe signal extraction ...."))
Try(system(extractCel))
Try(cat("Be patient...... ending probe signal extraction ...."))
#creating the box plot fro P and N
Try(tmp <- read.table("rawPN.txt", sep="\t", header=T))
Try(tmp.p <- tmp[which(tmp$probeset_id%in%p.ctrl$probeset_id), 8:dim(tmp)[2]])
Try(names(tmp.p) <- Targets$Name)
Try(tmp.p <- log2(tmp.p))
Try(tmp.n <- tmp[which(tmp$probeset_id%in%n.ctrl$probeset_id), 8:dim(tmp)[2]])
Try(names(tmp.n) <- Targets$Name)
Try(tmp.n <- log2(tmp.n))
Try(par(mfrow=c(1,2)))
Try(boxplot(tmp.p, main="Positive Ctrls", ylab="raw log2(intensity)", las=2))
Try(boxplot(tmp.n, main="Negative Ctrls", ylab="raw log2(intensity)", las=2))
Try(tkmessageBox(title="Raw probes intensities from CELs",message="Box plot of raw controls intensity data is available in main R window",icon="info"))
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="arrow"))
}
################################################################################
"qcMDS" <- function(){
# Try(require(edgeR) || stop("Missing edgeR library"))
Try(Targets <- get("Targets",envir=affylmGUIenvironment))
Try(whichArrayPlatform <- get("whichArrayPlatform",envir=affylmGUIenvironment))
if(whichArrayPlatform ==""){
Try(tkmessageBox(title="QC",message="No arrays have been loaded. Please try New or Open from the File menu.",type="ok",icon="error"))
Try(tkfocus(.affylmGUIglobals$ttMain))
Try(return())
}
if(affylmGUIenvironment$NormalizedAffyData.Available & affylmGUIenvironment$NGS.Available){
Try(NormalizedAffyData <- get("NormalizedAffyData", env=affylmGUIenvironment))
Try(mappedReads <- get("mappedReads", env=affylmGUIenvironment))
Try(targets <- get("Targets", env=affylmGUIenvironment))
} else Try(tkmessageBox(title="NGS data set",message="Normalized data are not available.", type="ok", icon="error"))
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="watch"))
cat("\ncreating the DGEList")
Try(NGSscaling.Available <- get("NGSscaling.Available", env=affylmGUIenvironment))
if(NGSscaling.Available){
Try(scaledReads <- get("NGSscaling", env=affylmGUIenvironment))
Try(mylist <- DGEList(counts= exprs(NormalizedAffyData), group=as.factor(targets$Target), lib.size=scaledReads))
} else {Try(mylist <- DGEList(counts= exprs(NormalizedAffyData), group=as.factor(targets$Target)))}
Try(mylist <- estimateCommonDisp(mylist))
Try(plotMDS.DGEList(mylist, labels=Targets$Name, main=paste("Multidimensional scaling plot\nCommon disp. after normalization",signif(mylist$common.dispersion,2),sep=" ")))
Try(tkmessageBox(title="Multdimensional scaling plot",message="Multidimensional scaling plot is available in main R window",icon="info"))
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="arrow"))
}
################################################################################
"EDAplotQuality" <- function(){
# require(EDASeq) || stop("Missing EDASeq library")
Try(whichArrayPlatform <- get("whichArrayPlatform",envir=affylmGUIenvironment))
if(whichArrayPlatform ==""){
Try(tkmessageBox(title="QC",message="No arrays have been loaded. Please try New or Open from the File menu.",type="ok",icon="error"))
Try(tkfocus(.affylmGUIglobals$ttMain))
Try(return())
}
if(affylmGUIenvironment$NormalizedAffyData.Available & affylmGUIenvironment$NGS.Available){
Try(NormalizedAffyData <- get("NormalizedAffyData", env=affylmGUIenvironment))
Try(targets <- get("Targets", env=affylmGUIenvironment))
} else Try(tkmessageBox(title="NGS data set",message="Normalized data are not available.", type="ok", icon="error"))
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="watch"))
Try(bfs <- BamFileList(targets$FileName))
Try(pd <- DataFrame("name"=targets$Name, "Target"= targets$Target, row.names=paste(targets$Name, targets$Target, sep=".")))
Try(elementMetadata(bfs) <- pd)
Try(plotQuality(bfs))
Try(legend("topright",unique(elementMetadata(bfs)[,1]),fill=rainbow(length(unique(elementMetadata(bfs)[,1])))))
Try(tkmessageBox(title="EDASeq Quality plot",message="EDASeq Quality plot is available in main R window",icon="info"))
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="arrow"))
}
################################################################################
"EDAreadNumber" <- function(){
# require(EDASeq) || stop("Missing EDASeq library")
Try(whichArrayPlatform <- get("whichArrayPlatform",envir=affylmGUIenvironment))
if(whichArrayPlatform ==""){
Try(tkmessageBox(title="QC",message="No arrays have been loaded. Please try New or Open from the File menu.",type="ok",icon="error"))
Try(tkfocus(.affylmGUIglobals$ttMain))
Try(return())
}
if(affylmGUIenvironment$NormalizedAffyData.Available & affylmGUIenvironment$NGS.Available){
Try(NormalizedAffyData <- get("NormalizedAffyData", env=affylmGUIenvironment))
Try(targets <- get("Targets", env=affylmGUIenvironment))
} else Try(tkmessageBox(title="NGS data set",message="Normalized data are not available.", type="ok", icon="error"))
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="watch"))
Try(bfs <- BamFileList(targets$FileName))
Try(pd <- DataFrame("name"=targets$Name, "Target"= targets$Target, row.names=paste(targets$Name, targets$Target, sep=".")))
Try(elementMetadata(bfs) <- pd)
Try(barplot(bfs, names.arg=unique(elementMetadata(bfs)[,1]),col=rainbow(length(unique(elementMetadata(bfs)[,1])))))
Try(tkmessageBox(title="EDASeq Read Number",message="EDASeq read number plot is available in main R window",icon="info"))
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="arrow"))
}
################################################################################
"EDANtFreq" <- function(){
# require(EDASeq) || stop("Missing EDASeq library")
Try(whichArrayPlatform <- get("whichArrayPlatform",envir=affylmGUIenvironment))
if(whichArrayPlatform ==""){
Try(tkmessageBox(title="QC",message="No arrays have been loaded. Please try New or Open from the File menu.",type="ok",icon="error"))
Try(tkfocus(.affylmGUIglobals$ttMain))
Try(return())
}
if(affylmGUIenvironment$NormalizedAffyData.Available & affylmGUIenvironment$NGS.Available){
Try(NormalizedAffyData <- get("NormalizedAffyData", env=affylmGUIenvironment))
Try(targets <- get("Targets", env=affylmGUIenvironment))
} else {
Try(tkmessageBox(title="NGS data set",message="Normalized data are not available.", type="ok", icon="error"))
Try(return())
}
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="watch"))
Try(bfs <- BamFileList(targets$FileName))
Try(pd <- DataFrame("name"=targets$Name, "Target"= targets$Target, row.names=paste(targets$Name, targets$Target, sep=".")))
Try(elementMetadata(bfs) <- pd)
Try(plot.names <- paste(unique(elementMetadata(bfs)[,1]), seq(1, length(unique(elementMetadata(bfs)[,1]))), sep=" = ", collapse=", "))
##selecting the bam to be plotted for mapping I.E. selecting the chromosome for the mapping
Try(ttcolExtract<-tktoplevel(.affylmGUIglobals$ttMain))
Try(tkwm.deiconify(ttcolExtract))
Try(tkgrab.set(ttcolExtract))
Try(tkfocus(ttcolExtract))
Try(tkwm.title(ttcolExtract,"Selecting the BAM file to be plotted"))
Try(tkgrid(tklabel(ttcolExtract,text=" ")))
Try(plotNtBam <- "")
Try(Local.colExtract <- tclVar(init=plotNtBam))
Try(entry.colExtract <-tkentry(ttcolExtract,width="4",font=.affylmGUIglobals$affylmGUIfont2,textvariable=Local.colExtract,bg="white"))
Try(tkgrid(tklabel(ttcolExtract,text=paste("Please enter the number associated to the sample of of interest\n", plot.names),font=.affylmGUIglobals$affylmGUIfont2)))
Try(tkgrid(entry.colExtract))
onOK <- function()
{
Try(assign("plotNtBam", as.numeric(tclvalue(Local.colExtract)),affylmGUIenvironment))
Try(tkgrab.release(ttcolExtract));Try(tkdestroy(ttcolExtract));Try(tkfocus(.affylmGUIglobals$ttMain))
}
Try(OK.but <-tkbutton(ttcolExtract,text=" OK ",command=onOK,font=.affylmGUIglobals$affylmGUIfont2))
Try(tkgrid(tklabel(ttcolExtract,text=" ")))
Try(tkgrid(OK.but))
Try(tkgrid.configure(OK.but))
Try(tkgrid(tklabel(ttcolExtract,text=" ")))
Try(tkfocus(entry.colExtract))
Try(tkbind(entry.colExtract, "<Return>",onOK))
Try(tkbind(ttcolExtract, "<Destroy>", function(){Try(tkgrab.release(ttcolExtract));Try(tkfocus(.affylmGUIglobals$ttMain));return(0)}))
Try(tkwait.window(ttcolExtract))
Try(tkfocus(.affylmGUIglobals$ttMain))
Try(plotNtBam <- get("plotNtBam", affylmGUIenvironment))
Try(plotNtFrequency(bfs[[plotNtBam]], main=unique(elementMetadata(bfs)[plotNtBam,1])))
Try(tkmessageBox(title="EDASeq Nt frequency",message=paste("EDASeq Nt frequency plot for sample", unique(elementMetadata(bfs)[plotNtBam,1]),"is available in main R window",icon="info")))
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="arrow"))
}
################################################################################
"EDAboxplot" <- function(){
# Try(require(EDASeq) || stop("Missing EDASeq library"))
Try(whichArrayPlatform <- get("whichArrayPlatform",envir=affylmGUIenvironment))
if(whichArrayPlatform ==""){
Try(tkmessageBox(title="QC",message="No arrays have been loaded. Please try New or Open from the File menu.",type="ok",icon="error"))
Try(tkfocus(.affylmGUIglobals$ttMain))
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="arrow"))
Try(return())
}
if(affylmGUIenvironment$NormalizedAffyData.Available & affylmGUIenvironment$NGS.Available){
Try(NormalizedAffyData <- get("NormalizedAffyData", env=affylmGUIenvironment))
Try(Targets <- get("Targets", env=affylmGUIenvironment))
} else {
Try(tkmessageBox(title="NGS data set",message="Normalized data are not available.", type="ok", icon="error"))
Try(return())
}
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="watch"))
Try(bowtieDirAvailable <- get("whichArrayPlatform",envir=affylmGUIenvironment))
Try(bowtieDirLocation.Available <- get("bowtieDirLocation.Available",envir=affylmGUIenvironment))
if(bowtieDirLocation.Available){
Try(bowtieDirLocation <- get("bowtieDirLocation",envir=affylmGUIenvironment))
} else{
Try(tkmessageBox(title="Bowtie data",message="It seems that Bowtie dir is missing!\nPlease install Bowtie using the function in General Tools menu",icon="error"))
Try(return())
}
#adding gc content to eset
Try(whichGenome <- annotation(NormalizedAffyData))
if(whichGenome == ""){
Try(tkmessageBox(title="Genome selection",message="No genome is indicated in the annotation slot of ExpressionSet",type="ok", icon="error"))
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="arrow"))
Try(return())
} else if (whichGenome == "hs19"){
Try(annlibname <- system.file("bowtie/hg19_gene-level.scaffold.Rda",package="oneChannelGUI"))
Try(load(annlibname))
} else if (whichGenome == "mm9"){
Try(annlibname <- system.file("bowtie/mm9_gene-level.scaffold.Rda",package="oneChannelGUI"))
Try(load(annlibname))
} else if (whichGenome == "rn4"){
Try(annlibname <- system.file("bowtie/rn4_gene-level.scaffold.Rda",package="oneChannelGUI"))
Try(load(annlibname))
} else{
Try(tkmessageBox(title="Genome selection",message="In the annotation slot of ExpressionSet is present a genome not annotated in oneChannelGUI!\nContact the maintainer for Genome implementation",type="ok", icon="error"))
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="arrow"))
Try(return())
}
#detecting the chr under analysis
Try(chr <- strsplit(Targets$FileName[1], "_")) #getting the chr
Try(chr <- as.vector(unlist(chr)))
Try(chr <- chr[length(chr)])
Try(chr <- sub(".bam", "", chr)) #needed to extract the right subset of gene-level annotation from makeGeneScaffold generated GRanges list
Try(chr <- sub("chr0", "chr", chr))
#selecting the chromosome genomic reanges on which assigning BAM data
Try(chr.gr <- chr.gr[which(names(chr.gr) == chr)])
Try(genes.lenght <- width(ranges(chr.gr[[1]])))
Try(names(genes.lenght) <- elementMetadata(chr.gr[[1]])$names)
Try(gc.freq <- gc.freq[which(names(gc.freq) == chr)])
Try(gc.freq <- unlist(gc.freq))
Try(tmp.names <- names(gc.freq))
Try(tmp.names <- sapply(tmp.names,function(x,chr){tmp<-sub(chr,'',x);return(tmp)},chr=paste(chr,'.', sep="")))
Try(tmp.names <- as.character(tmp.names))
Try(names(gc.freq) <- tmp.names)
if(identical(names(genes.lenght), names(gc.freq))){
Try(feature <- data.frame(gc=gc.freq,length=genes.lenght))
}else{
Try(gc.freq <- gc.freq[order(names(gc.freq))])
Try(genes.lenght <- genes.lenght[order(names(genes.lenght))])
Try(feature <- data.frame(gc=gc.freq,length=genes.lenght))
}
Try(var.tmp.pd<-data.frame(names(feature)))
Try(names(var.tmp.pd)<-"labelDescription" )
Try(rownames(var.tmp.pd)<-names(feature))
Try(tmp1.pd<-new("AnnotatedDataFrame", data=feature, varMetadata=var.tmp.pd))
#making eset featureNames identical to names gc.freq and genes.length
.myFeature <- function(eset){
tmp.names <- featureNames(NormalizedAffyData)
tmp.names <- sapply(tmp.names, function(x){sub('\\-_','#',x)})
tmp.names <- as.character(tmp.names)
tmp.names <- sapply(tmp.names, function(x){sub('\\+_','#',x)})
tmp.names <- as.character(tmp.names)
tmp.names <- sapply(tmp.names, function(x){tmp <- strsplit(x, '#');return(tmp[[1]][2])})
tmp.names <- as.character(tmp.names)
return(tmp.names)
}
Try(counts <- NormalizedAffyData)
Try(featureNames(counts) <- .myFeature(NormalizedAffyData))
Try(tmp1.pd <- tmp1.pd[which(featureNames(tmp1.pd)%in%featureNames(counts)),])
Try(counts <- counts[which(featureNames(counts)%in%featureNames(tmp1.pd)),])
Try(counts <- counts[order(featureNames(counts)),])
Try(tmp1.pd <- tmp1.pd[order(featureNames(tmp1.pd)),])
Try(eseq <- newSeqExpressionSet(exprs(counts), phenoData=pData(counts), featureData=tmp1.pd))
Try(names(pData(eseq))[1] <- "conditions")
Try(tkmessageBox(title="EDASeq Boxplot",message="Sample boxplot is available in main R window",icon="info"))
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="arrow"))
Try(boxplot(eseq, ylab="log10 counts"))
}
################################################################################
"EDAbiasPlot" <- function(){
# Try(require(EDASeq) || stop("Missing EDASeq library"))
Try(whichArrayPlatform <- get("whichArrayPlatform",envir=affylmGUIenvironment))
if(whichArrayPlatform ==""){
Try(tkmessageBox(title="QC",message="No arrays have been loaded. Please try New or Open from the File menu.",type="ok",icon="error"))
Try(tkfocus(.affylmGUIglobals$ttMain))
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="arrow"))
Try(return())
}
if(affylmGUIenvironment$NormalizedAffyData.Available & affylmGUIenvironment$NGS.Available){
Try(NormalizedAffyData <- get("NormalizedAffyData", env=affylmGUIenvironment))
Try(Targets <- get("Targets", env=affylmGUIenvironment))
} else {
Try(tkmessageBox(title="NGS data set",message="Normalized data are not available.", type="ok", icon="error"))
Try(return())
}
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="watch"))
Try(bowtieDirAvailable <- get("whichArrayPlatform",envir=affylmGUIenvironment))
Try(bowtieDirLocation.Available <- get("bowtieDirLocation.Available",envir=affylmGUIenvironment))
if(bowtieDirLocation.Available){
Try(bowtieDirLocation <- get("bowtieDirLocation",envir=affylmGUIenvironment))
} else{
Try(tkmessageBox(title="Bowtie data",message="It seems that Bowtie dir is missing!\nPlease install Bowtie using the function in General Tools menu",icon="error"))
Try(return())
}
#adding gc content to eset
Try(whichGenome <- annotation(NormalizedAffyData))
if(whichGenome == ""){
Try(tkmessageBox(title="Genome selection",message="No genome is indicated in the annotation slot of ExpressionSet",type="ok", icon="error"))
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="arrow"))
Try(return())
} else if (whichGenome == "hs19"){
Try(annlibname <- system.file("bowtie/hg19_gene-level.scaffold.Rda",package="oneChannelGUI"))
Try(load(annlibname))
} else if (whichGenome == "mm9"){
Try(annlibname <- system.file("bowtie/mm9_gene-level.scaffold.Rda",package="oneChannelGUI"))
Try(load(annlibname))
} else if (whichGenome == "rn4"){
Try(annlibname <- system.file("bowtie/rn4_gene-level.scaffold.Rda",package="oneChannelGUI"))
Try(load(annlibname))
} else{
Try(tkmessageBox(title="Genome selection",message="In the annotation slot of ExpressionSet is present a genome not annotated in oneChannelGUI!\nContact the maintainer for Genome implementation",type="ok", icon="error"))
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="arrow"))
Try(return())
}
#detecting the chr under analysis
Try(chr <- strsplit(Targets$FileName[1], "_")) #getting the chr
Try(chr <- as.vector(unlist(chr)))
Try(chr <- chr[length(chr)])
Try(chr <- sub(".bam", "", chr)) #needed to extract the right subset of gene-level annotation from makeGeneScaffold generated GRanges list
Try(chr <- sub("chr0", "chr", chr))
#selecting the chromosome genomic reanges on which assigning BAM data
Try(chr.gr <- chr.gr[which(names(chr.gr) == chr)])
Try(genes.lenght <- width(ranges(chr.gr[[1]])))
Try(names(genes.lenght) <- elementMetadata(chr.gr[[1]])$names)
Try(gc.freq <- gc.freq[which(names(gc.freq) == chr)])
Try(gc.freq <- unlist(gc.freq))
Try(tmp.names <- names(gc.freq))
Try(tmp.names <- sapply(tmp.names,function(x,chr){tmp<-sub(chr,'',x);return(tmp)},chr=paste(chr,'.', sep="")))
Try(tmp.names <- as.character(tmp.names))
Try(names(gc.freq) <- tmp.names)
if(identical(names(genes.lenght), names(gc.freq))){
Try(feature <- data.frame(gc=gc.freq,length=genes.lenght))
}else{
Try(gc.freq <- gc.freq[order(names(gc.freq))])
Try(genes.lenght <- genes.lenght[order(names(genes.lenght))])
Try(feature <- data.frame(gc=gc.freq,length=genes.lenght))
}
Try(var.tmp.pd<-data.frame(names(feature)))
Try(names(var.tmp.pd)<-"labelDescription" )
Try(rownames(var.tmp.pd)<-names(feature))
Try(tmp1.pd<-new("AnnotatedDataFrame", data=feature, varMetadata=var.tmp.pd))
#making eset featureNames identical to names gc.freq and genes.length
.myFeature <- function(eset){
tmp.names <- featureNames(NormalizedAffyData)
tmp.names <- sapply(tmp.names, function(x){sub('\\-_','#',x)})
tmp.names <- as.character(tmp.names)
tmp.names <- sapply(tmp.names, function(x){sub('\\+_','#',x)})
tmp.names <- as.character(tmp.names)
tmp.names <- sapply(tmp.names, function(x){tmp <- strsplit(x, '#');return(tmp[[1]][2])})
tmp.names <- as.character(tmp.names)
return(tmp.names)
}
Try(counts <- NormalizedAffyData)
Try(featureNames(counts) <- .myFeature(NormalizedAffyData))
Try(tmp1.pd <- tmp1.pd[which(featureNames(tmp1.pd)%in%featureNames(counts)),])
Try(counts <- counts[which(featureNames(counts)%in%featureNames(tmp1.pd)),])
Try(counts <- counts[order(featureNames(counts)),])
Try(tmp1.pd <- tmp1.pd[order(featureNames(tmp1.pd)),])
Try(eseq <- newSeqExpressionSet(exprs(counts), phenoData=pData(counts), featureData=tmp1.pd))
Try(names(pData(eseq))[1] <- "conditions")
Try(tkmessageBox(title="EDASeq Bias Plot",message="Sample bias plot is available in main R window",icon="info"))
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="arrow"))
Try(par(mfrow=c(2,2)))
#low resolution plot
Try(biasPlot(eseq, "gc", log=T, ylim=c(0,5)))
Try(biasPlot(eseq, "length", log=T, ylim=c(0,5)))
#high resolution plot
Try(biasPlot(eseq, "gc", log=T))
Try(biasPlot(eseq, "length", log=T))
}
###########################################################################################################
"fastQC" <-function(){
Try(binDir <- get("binDir",envir=affylmGUIenvironment))
Try(system(paste(binDir,"/fastqc",sep="")))
}
###########################################################################################################
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oneChannelGUI documentation built on Nov. 17, 2017, 11:02 a.m.
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Defines functions delta.plot1 PlotOptionsv1 affyPlotMA
Documented in affyPlotMA PlotOptionsv1
#set of functions, directly/indirectly involved, in oneChannelGUI qcMenu
#oneChannelGUI normBoxplot this function produces a boxplot for NormalizedAffyData
#oneChannelGUI ocPlotPCA this function produces a PCA plot using the normalized expression data works both with affy and exon arrays
#oneChannelGUI ocPlotHist this function produces an affy hist plot for exon and gene level data after probeset intenisty calculation
#oneChannelGUI sample.size.evaluation allows sample size and statistical power estimation using the ssize package
#oneChannelGUI sample.size.evaluation1 allows sample size and statistical power estimation using the sizepower package
#oneChannelGUI PlotOptionsv1 plotting optino selections
#affyPlotMA modified to use the expr(NormalizedAffyData)
#oneChannelGUI rawBoxplotPN plot the raw log2 intensity values for positive and negative ctrls extracted from CEL files
#oneChannelGUI qcMDS evaluating the presence eof outliers using plotMDS.dge of NGS data
#oneChannelGUI EDAplotQuality bam qc associated to EDASeq
# EDAreadNumber
# EDANtFreq
# EDAboxplot
# EDAbiasPlot
# oneChannelGUI fastQC java tool to evaluate fastq quality
################################################################################
"normBoxplot" <- function(){
#error if no data are loaded
Try(whichArrayPlatform <- get("whichArrayPlatform",envir=affylmGUIenvironment))
if(whichArrayPlatform ==""){
Try(tkmessageBox(title="QC",message="No arrays have been loaded. Please try New or Open from the File menu.",type="ok",icon="error"))
Try(tkfocus(.affylmGUIglobals$ttMain))
Try(return())
}
#########################
if(whichArrayPlatform=="LARGE" || whichArrayPlatform=="GENE" || whichArrayPlatform=="ILLU"){
if(affylmGUIenvironment$NormalizedAffyData.Available){
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="watch"))
Try(NormalizedAffyData <- get("NormalizedAffyData",envir=affylmGUIenvironment))
Try( boxplot(as.data.frame(exprs(NormalizedAffyData)), las=2, names=pData(NormalizedAffyData)$Name,ylab="Normalized log2(intensities)"))
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="arrow"))
}
} else if (whichArrayPlatform=="AFFY"){
if(affylmGUIenvironment$NormalizedAffyData.Available){
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="watch"))
Try(NormalizedAffyData <- get("NormalizedAffyData",envir=affylmGUIenvironment))
Try( boxplot(as.data.frame(exprs(NormalizedAffyData)), las=2, names=pData(NormalizedAffyData)$Name,ylab="Normalized log2(intensities)"))
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="arrow"))
}
} else if (whichArrayPlatform=="NGS"){
if(affylmGUIenvironment$NormalizedAffyData.Available){
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="watch"))
Try(NormalizedAffyData <- get("NormalizedAffyData",envir=affylmGUIenvironment))
Try( boxplot(as.data.frame(log10(exprs(NormalizedAffyData))), las=2, names=pData(NormalizedAffyData)$Name,ylab="log10 peaks counts"))
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="arrow"))
}
} else{
Try(tkmessageBox(title="Box plot normalized data",message="Probe set summary is not available!\nNext menu will give options for probe set summarization", type="ok", icon="info"))
Try(NormalizeNow())
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="watch"))
Try(NormalizedAffyData <- get("NormalizedAffyData",envir=affylmGUIenvironment))
Try( boxplot(as.data.frame(exprs(NormalizedAffyData)), las=2, names=pData(NormalizedAffyData)$Name,ylab="Normalized log2(intensities)"))
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="arrow"))
}
}
################################################################################
#run the affycoretool plotPCA
"ocPlotPCA" <- function(){
#error if no data are loaded
Try(whichArrayPlatform <- get("whichArrayPlatform",envir=affylmGUIenvironment))
if(whichArrayPlatform ==""){
Try(tkmessageBox(title="QC",message="No arrays have been loaded. Please try New or Open from the File menu.",type="ok",icon="error"))
Try(tkfocus(.affylmGUIglobals$ttMain))
Try(return())
}
#########################
#plotPCA was derived by affycoretools they desapeared in relase 2.0
"plotPCA" <- function (eset, groups = NULL, groupnames = NULL, addtext = NULL,
x.coord = NULL, y.coord = NULL, screeplot = FALSE, squarepca = FALSE,
pch = NULL, col = NULL, title=NULL,...) {
if (is.null(groupnames)) groupnames <- sampleNames(eset)
if (is.factor(groupnames)) groupnames <- as.character(groupnames)
pca <- prcomp(t(exprs(eset)))
x <- exprs(eset)
dimnames(x)[[2]] <- groupnames
hc <- hclust(dist(t(x)), "ave")
if (screeplot) {
plot(pca, main = title)
} else {
if (squarepca) {
ylim <- max(abs(range(pca$x[, 1])))
ylim <- c(-ylim, ylim)
} else ylim <- NULL
if (!is.null(groups)) {
if (is.null(pch)) pch <- groups
if (is.null(col)) col <- groups
plot(pca$x[, 1:2], pch = pch, col = col, ylab = "PC2", xlab = "PC1", main = title, ylim = ylim, ...)
} else {
if (is.null(pch)) pch <- ""
if (is.null(col)) col <- 1:length(groupnames)
par(mfrow=c(1,3))
plot(pca, main="PCs information content")
plot(pca$x[, 1:2], pch = pch, ylab = "PC2", xlab = "PC1", main = title, ylim = ylim, ...)
text(pca$x[, 1:2], groupnames, col= col <- 1:length(groupnames) , cex=0.7)
plot(hc, main="Samples HCL", xlab="")
}
}
}
Try(whichArrayPlatform <- get("whichArrayPlatform",envir=affylmGUIenvironment))
if(whichArrayPlatform=="EXON"){
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="watch"))
if(affylmGUIenvironment$exonAffyData.Available){
##makning the menu for selecting gene or exon level density plot
Try(ttGeneExonMethod <- tktoplevel(.affylmGUIglobals$ttMain))
Try(tkwm.deiconify(ttGeneExonMethod))
Try(tkgrab.set(ttGeneExonMethod))
Try(tkfocus(ttGeneExonMethod))
Try(tkwm.title(ttGeneExonMethod,"Gene/Exon level plots"))
Try(tkgrid(tklabel(ttGeneExonMethod,text=" ")))
Try(ttGeneExonMethodTcl <- tclVar("gene"))
Try(rbGene <- tkradiobutton(ttGeneExonMethod,text="Gene levels",variable=ttGeneExonMethodTcl,value="gene",font=.affylmGUIglobals$affylmGUIfont2))
Try(rbExon<-tkradiobutton(ttGeneExonMethod,text="Exon levels",variable=ttGeneExonMethodTcl,value="exon",font=.affylmGUIglobals$affylmGUIfont2))
Try(tkgrid(tklabel(ttGeneExonMethod,text=" "),rbGene))
Try(tkgrid(tklabel(ttGeneExonMethod,text=" "),rbExon))
Try(tkgrid.configure(rbGene,rbExon,columnspan=2,sticky="w"))
Try(tkgrid(tklabel(ttGeneExonMethod,text=" "),tklabel(ttGeneExonMethod,text=" ")))
Try(ReturnVal <- "")
Try(onCancel <- function() {Try(ReturnVal <<- "");Try(tkgrab.release(ttGeneExonMethod));Try(tkdestroy(ttGeneExonMethod));Try(tkfocus(.affylmGUIglobals$ttMain))})
Try(onOK <- function() {Try(ReturnVal <<- tclvalue(ttGeneExonMethodTcl));Try(tkgrab.release(ttGeneExonMethod));Try(tkdestroy(ttGeneExonMethod));Try(tkfocus(.affylmGUIglobals$ttMain))})
Try(OK.but <- tkbutton(ttGeneExonMethod,text="OK",command=onOK,font=.affylmGUIglobals$affylmGUIfont2))
Try(Cancel.but <- tkbutton(ttGeneExonMethod,text="Cancel",command=onCancel,font=.affylmGUIglobals$affylmGUIfont2))
Try(tkgrid(tklabel(ttGeneExonMethod,text=" "),OK.but,Cancel.but,tklabel(ttGeneExonMethod,text=" ")))
Try(tkgrid.configure(OK.but,sticky="e"))
Try(tkgrid.configure(Cancel.but,sticky="w"))
Try(tkgrid(tklabel(ttGeneExonMethod,text=" ")))
Try(tkbind(ttGeneExonMethod,"<Destroy>",function() {ReturnVal <- "";Try(tkgrab.release(ttGeneExonMethod));Try(tkfocus(.affylmGUIglobals$ttMain));}))
Try(tkbind(OK.but, "<Return>",onOK))
Try(tkbind(Cancel.but, "<Return>",onCancel))
Try(tkwait.window(ttGeneExonMethod))
if(ReturnVal=="gene"){
Try(NormalizedAffyData <- get("NormalizedAffyData",envir=affylmGUIenvironment))
Try(plotPCA(NormalizedAffyData, groupnames= affylmGUIenvironment$Targets$Name, title="Gene level PCA"))
} else if (ReturnVal=="exon"){
Try(exonAffyData <- get("exonAffyData",envir=affylmGUIenvironment))
Try(plotPCA(exonAffyData, groupnames= affylmGUIenvironment$Targets$Name, title="Exon level PCA"))
} else {
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="arrow"))
Try(return())
}
} else{
Try(tkmessageBox(title="Gene level PCA/HCL",message="No exon data are available! These data seem not to be exon arrays data",type="ok",icon="error"))
}
Try(tkmessageBox(title="Exon level PCA/HCL",message=paste("Plots will be displayed in the main R window")))
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="arrow"))
}
if(whichArrayPlatform=="AFFY"){
if(affylmGUIenvironment$NormalizedAffyData.Available){
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="watch"))
Try(NormalizedAffyData <- get("NormalizedAffyData",envir=affylmGUIenvironment))
Try(plotPCA(NormalizedAffyData, groupnames= affylmGUIenvironment$Targets$Name, title="Samples PCA plot"))
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="arrow"))
} else{
Try(tkmessageBox(title="plotPCA",message="Probe set summary is not available!\nNext menu will give options for probe set summarization", type="ok", icon="info"))
Try(NormalizeNow())
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="watch"))
Try(NormalizedAffyData <- get("NormalizedAffyData",envir=affylmGUIenvironment))
Try(plotPCA(NormalizedAffyData, groupnames= affylmGUIenvironment$Targets$Name, title="Samples PCA plot"))
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="arrow"))
}
}
if(whichArrayPlatform=="LARGE" || whichArrayPlatform=="GENE" || whichArrayPlatform=="ILLU" || whichArrayPlatform=="NGS"){
if(affylmGUIenvironment$NormalizedAffyData.Available){
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="watch"))
Try(NormalizedAffyData <- get("NormalizedAffyData",envir=affylmGUIenvironment))
Try(plotPCA(NormalizedAffyData, groupnames= affylmGUIenvironment$Targets$Name, title="Samples PCA plot"))
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="arrow"))
} else{
Try(tkmessageBox(title="plotPCA",message="Probe set summary is not available!", type="ok", icon="error"))
}
}
}
################################################################################
#this function will plot density plot for the gene and exon expression loaded in oneChannelGUI
#modify plotHist function from affycoretools
"ocPlotHist" <- function(){
#error if no data are loaded
Try(whichArrayPlatform <- get("whichArrayPlatform",envir=affylmGUIenvironment))
if(whichArrayPlatform ==""){
Try(tkmessageBox(title="QC",message="No arrays have been loaded. Please try New or Open from the File menu.",type="ok",icon="error"))
Try(tkfocus(.affylmGUIglobals$ttMain))
Try(return())
}
#########################
plotHist<- function (dat, filenames = NULL, title=NULL)
{
if (is.null(filenames))
filenames <- sampleNames(dat)
cl <- make.cl(filenames)
if (length(filenames) <= 8) {
if (is(dat, "ExpressionSet"))
plotDensity(as.matrix(exprs(dat)), lty = cl, lwd = 2, col = 1:length(filenames), main=title)
x.ax <- legend(1, 1, legend = filenames, lty = 1, lwd = 2,
col = cl, plot = FALSE)$rect$w
legend(par("usr")[2] - (par("usr")[2] - par("usr")[1])/100 -
x.ax, par("usr")[4] - (par("usr")[4] - par("usr")[3])/100,
legend = filenames, lty = 1, lwd = 2, col = cl)
}
else {
if (is(dat, "ExpressionSet"))
plotDensity(as.matrix(exprs(dat)), lty = cl, lwd = 2, col = 1:length(filenames), main=title)
x.ax <- legend(1, 1, legend = filenames, lty = 1, lwd = 2,
col = cl, plot = FALSE)$rect$w
y.ax <- legend(1, 1, legend = filenames, lty = 1, lwd = 2,
col = cl, plot = FALSE)$rect$h
ydiff <- par("usr")[4] - par("usr")[3]
if (y.ax < ydiff) {
legend(par("usr")[2] - (par("usr")[2] - par("usr")[1])/100 -
x.ax, par("usr")[4] - (par("usr")[4] - par("usr")[3])/100,
legend = filenames, lty = cl, lwd = 2, col = 1:length(filenames))
}
else {
cexval <- 1
while (y.ax > ydiff) {
cexval <- cexval - 0.05
y.ax <- legend(1, 1, legend = filenames, lty = 1,
lwd = 2, col = cl, plot = FALSE, cex = cexval)$rect$h
x.ax <- legend(1, 1, legend = filenames, lty = 1,
lwd = 2, col = cl, plot = FALSE, cex = cexval)$rect$w
}
legend(par("usr")[2] - (par("usr")[2] - par("usr")[1])/100 -
x.ax, par("usr")[4] - (par("usr")[4] - par("usr")[3])/100,
legend = filenames, lty = cl, lwd = 2, col = 1:length(filenames),
cex = cexval)
}
}
}
make.cl <- function(filenames){
## A function to make a classlabel for plotting
## Check for number of files
if(length(filenames) <= 8)
cl <- 1 : length(filenames)
if(length(filenames) > 8){
mod <- floor(length(filenames)/8)
cl <- NULL
for(i in 1 : mod){
cl <- c(cl, rep(i, 8))
}
rem <- length(filenames) - mod*8
cl <- c(cl, rep(mod + 1, rem))
}
cl
}
if(affylmGUIenvironment$exonAffyData.Available){
##makning the menu for selecting gene or exon level density plot
Try(ttGeneExonMethod <- tktoplevel(.affylmGUIglobals$ttMain))
Try(tkwm.deiconify(ttGeneExonMethod))
Try(tkgrab.set(ttGeneExonMethod))
Try(tkfocus(ttGeneExonMethod))
Try(tkwm.title(ttGeneExonMethod,"Gene/Exon level plots"))
Try(tkgrid(tklabel(ttGeneExonMethod,text=" ")))
Try(ttGeneExonMethodTcl <- tclVar("gene"))
Try(rbGene <- tkradiobutton(ttGeneExonMethod,text="Gene levels",variable=ttGeneExonMethodTcl,value="gene",font=.affylmGUIglobals$affylmGUIfont2))
Try(rbExon<-tkradiobutton(ttGeneExonMethod,text="Exon levels",variable=ttGeneExonMethodTcl,value="exon",font=.affylmGUIglobals$affylmGUIfont2))
Try(tkgrid(tklabel(ttGeneExonMethod,text=" "),rbGene))
Try(tkgrid(tklabel(ttGeneExonMethod,text=" "),rbExon))
Try(tkgrid.configure(rbGene,rbExon,columnspan=2,sticky="w"))
Try(tkgrid(tklabel(ttGeneExonMethod,text=" "),tklabel(ttGeneExonMethod,text=" ")))
Try(ReturnVal <- "")
Try(onCancel <- function() {Try(ReturnVal <<- "");Try(tkgrab.release(ttGeneExonMethod));Try(tkdestroy(ttGeneExonMethod));Try(tkfocus(.affylmGUIglobals$ttMain))})
Try(onOK <- function() {Try(ReturnVal <<- tclvalue(ttGeneExonMethodTcl));Try(tkgrab.release(ttGeneExonMethod));Try(tkdestroy(ttGeneExonMethod));Try(tkfocus(.affylmGUIglobals$ttMain))})
Try(OK.but <- tkbutton(ttGeneExonMethod,text="OK",command=onOK,font=.affylmGUIglobals$affylmGUIfont2))
Try(Cancel.but <- tkbutton(ttGeneExonMethod,text="Cancel",command=onCancel,font=.affylmGUIglobals$affylmGUIfont2))
Try(tkgrid(tklabel(ttGeneExonMethod,text=" "),OK.but,Cancel.but,tklabel(ttGeneExonMethod,text=" ")))
Try(tkgrid.configure(OK.but,sticky="e"))
Try(tkgrid.configure(Cancel.but,sticky="w"))
Try(tkgrid(tklabel(ttGeneExonMethod,text=" ")))
Try(tkbind(ttGeneExonMethod,"<Destroy>",function() {ReturnVal <- "";Try(tkgrab.release(ttGeneExonMethod));Try(tkfocus(.affylmGUIglobals$ttMain));}))
Try(tkbind(OK.but, "<Return>",onOK))
Try(tkbind(Cancel.but, "<Return>",onCancel))
Try(tkwait.window(ttGeneExonMethod))
if(ReturnVal=="gene"){
Try(NormalizedAffyData <- get("NormalizedAffyData",envir=affylmGUIenvironment))
plotHist(NormalizedAffyData, title="Gene level density plot")
} else if (ReturnVal=="exon") {
Try(exonAffyData <- get("exonAffyData",envir=affylmGUIenvironment))
plotHist(exonAffyData, title="Exon level density plot")
} else {
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="arrow"))
Try(return())
}
}
else{
Try(tkmessageBox(title="Gene/Exon level Histograms",message="No exon data are available! These data seem not to be exon arrays data",type="ok",icon="error"))
}
Try(tkmessageBox(title="Gene/Exon level Histograms",message=paste("Plots will be displayed in the main R window")))
}
################################################################################
#part of the functions used to evaluate sample size and statistical power estimation
# sd distribution
"sample.size.evaluation" <- function(){
# require(multtest) || stop("library multtest could not be found !")
# require(ssize) || stop("library ssize could not be found !")
#error if no data are loaded
Try(whichArrayPlatform <- get("whichArrayPlatform",envir=affylmGUIenvironment))
if(whichArrayPlatform ==""){
Try(tkmessageBox(title="Study design",message="No arrays have been loaded. Please try New or Open from the File menu.",type="ok",icon="error"))
Try(tkfocus(.affylmGUIglobals$ttMain))
Try(return())
}
#########################
if(whichArrayPlatform =="EXON"){
Try(NormalizedAffyData <- get("NormalizedAffyData", env=affylmGUIenvironment))
}else{
if(affylmGUIenvironment$NormalizedAffyData.Available){
Try(NormalizedAffyData <- get("NormalizedAffyData", env=affylmGUIenvironment))
} else {
Try(tkmessageBox(title="Sample size & Power plots",message="Normalized data are not available.\n Please calculate the probe set expression summaries ", type="ok", icon="error"))
Try(return())
}
}
Try(expression.values <- exprs(NormalizedAffyData))
#assigning fold.change graphical menu
Try(ttGetFC<-tktoplevel(.affylmGUIglobals$ttMain))
Try(tkwm.deiconify(ttGetFC))
Try(tkgrab.set(ttGetFC))
Try(tkfocus(ttGetFC))
Try(tkwm.title(ttGetFC,"Assigning Fold Change"))
Try(tkgrid(tklabel(ttGetFC,text=" ")))
Try(FCnum <- "")
Try(Local.FC <- tclVar(init=FCnum))
Try(entry.FC <-tkentry(ttGetFC,width="3",font=.affylmGUIglobals$affylmGUIfont2,textvariable=Local.FC,bg="white"))
Try(tkgrid(tklabel(ttGetFC,text="Please Fold Change value.",font=.affylmGUIglobals$affylmGUIfont2)))
Try(tkgrid(entry.FC))
onOK <- function()
{
Try(FCnum <- as.numeric(tclvalue(Local.FC)))
if(nchar(FCnum)==0)
FCnum <- "Unselected"
Try(assign("FCnum",FCnum,affylmGUIenvironment))
Try(tclvalue(.affylmGUIglobals$FCTcl) <- FCnum)
Try(tkgrab.release(ttGetFC));Try(tkdestroy(ttGetFC));Try(tkfocus(.affylmGUIglobals$ttMain))
}
Try(OK.but <-tkbutton(ttGetFC,text=" OK ",command=onOK,font=.affylmGUIglobals$affylmGUIfont2))
Try(tkgrid(tklabel(ttGetFC,text=" ")))
Try(tkgrid(OK.but))
Try(tkgrid.configure(OK.but))
Try(tkgrid(tklabel(ttGetFC,text=" ")))
Try(tkfocus(entry.FC))
Try(tkbind(entry.FC, "<Return>",onOK))
Try(tkbind(ttGetFC, "<Destroy>", function(){Try(tkgrab.release(ttGetFC));Try(tkfocus(.affylmGUIglobals$ttMain));return(0)}))
Try(tkwait.window(ttGetFC))
Try(tkfocus(.affylmGUIglobals$ttMain))
if(FCnum == "Unselected"){
Try(tkmessageBox(title="Sample size & Power plots",message="Fold change threshold was not selected.\nAborting analysis.", type="ok", icon="error"))
Try(return())
}
#######################################################Ã Ã
#assigning power and sig.level grphical menu
Try(ttGetPower<-tktoplevel(.affylmGUIglobals$ttMain))
Try(tkwm.deiconify(ttGetPower))
Try(tkgrab.set(ttGetPower))
Try(tkfocus(ttGetPower))
Try(tkwm.title(ttGetPower,"Assigning the Statistical Power"))
Try(tkgrid(tklabel(ttGetPower,text=" ")))
Try(Powernum <- "")
Try(Local.Power <- tclVar(init=Powernum))
Try(entry.Power <-tkentry(ttGetPower,width="3",font=.affylmGUIglobals$affylmGUIfont2,textvariable=Local.Power,bg="white"))
Try(tkgrid(tklabel(ttGetPower,text="Please assign a Power value, \ni.e. any value between 0 and 1",font=.affylmGUIglobals$affylmGUIfont2)))
Try(tkgrid(entry.Power))
onOK <- function()
{
Try(Powernum <- as.numeric(tclvalue(Local.Power)))
if(nchar(Powernum)==0)
Powernum <- "Unselected"
Try(assign("Powernum",Powernum,affylmGUIenvironment))
Try(tclvalue(.affylmGUIglobals$PowerTcl) <- Powernum)
Try(tkgrab.release(ttGetPower));Try(tkdestroy(ttGetPower));Try(tkfocus(.affylmGUIglobals$ttMain))
}
Try(OK.but <-tkbutton(ttGetPower,text=" OK ",command=onOK,font=.affylmGUIglobals$affylmGUIfont2))
Try(tkgrid(tklabel(ttGetPower,text=" ")))
Try(tkgrid(OK.but))
Try(tkgrid.configure(OK.but))
Try(tkgrid(tklabel(ttGetPower,text=" ")))
Try(tkfocus(entry.Power))
Try(tkbind(entry.Power, "<Return>",onOK))
Try(tkbind(ttGetPower, "<Destroy>", function(){Try(tkgrab.release(ttGetPower));Try(tkfocus(.affylmGUIglobals$ttMain));return(0)}))
Try(tkwait.window(ttGetPower))
Try(tkfocus(.affylmGUIglobals$ttMain))
if(Powernum == "Unselected"){
Try(tkmessageBox(title="Sample size & Power plots",message="Power threshold was not selected.\nAborting analysis.", type="ok", icon="error"))
Try(return())
}
#######################################################Ã Ã
#######################################################Ã Ã
#assigning power and sig.level grphical menu
Try(ttGetSL<-tktoplevel(.affylmGUIglobals$ttMain))
Try(tkwm.deiconify(ttGetSL))
Try(tkgrab.set(ttGetSL))
Try(tkfocus(ttGetSL))
Try(tkwm.title(ttGetSL,"Assigning the significance level"))
Try(tkgrid(tklabel(ttGetSL,text=" ")))
Try(SLnum <- "")
Try(Local.SL <- tclVar(init=SLnum))
Try(entry.SL <-tkentry(ttGetSL,width="4",font=.affylmGUIglobals$affylmGUIfont2,textvariable=Local.SL,bg="white"))
Try(tkgrid(tklabel(ttGetSL,text="Please assign the significance level, \n, i.e. 0.05 or lower",font=.affylmGUIglobals$affylmGUIfont2)))
Try(tkgrid(entry.SL))
onOK <- function()
{
Try(SLnum <- as.numeric(tclvalue(Local.SL)))
if(nchar(SLnum)==0)
SLnum <- "Unselected"
Try(assign("SLnum",SLnum,affylmGUIenvironment))
Try(tclvalue(.affylmGUIglobals$SLTcl) <- SLnum)
Try(tkgrab.release(ttGetSL));Try(tkdestroy(ttGetSL));Try(tkfocus(.affylmGUIglobals$ttMain))
}
Try(OK.but <-tkbutton(ttGetSL,text=" OK ",command=onOK,font=.affylmGUIglobals$affylmGUIfont2))
Try(tkgrid(tklabel(ttGetSL,text=" ")))
Try(tkgrid(OK.but))
Try(tkgrid.configure(OK.but))
Try(tkgrid(tklabel(ttGetSL,text=" ")))
Try(tkfocus(entry.SL))
Try(tkbind(entry.SL, "<Return>",onOK))
Try(tkbind(ttGetSL, "<Destroy>", function(){Try(tkgrab.release(ttGetSL));Try(tkfocus(.affylmGUIglobals$ttMain));return(0)}))
Try(tkwait.window(ttGetSL))
Try(tkfocus(.affylmGUIglobals$ttMain))
if(SLnum == "Unselected"){
Try(tkmessageBox(title="Sample size & Power plots",message="Significance threshold was not selected.\nAborting analysis.", type="ok", icon="error"))
Try(return())
}
#######################################################Ã Ã
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="watch"))
Try(common.sd<-function(x){
covariate.data <<- affylmGUIenvironment$Targets$Target
target.unique <- unique(covariate.data)
common.sd1<- sqrt((sd(x[which(covariate.data==target.unique[1])])^2*(length(which(covariate.data==target.unique[1]))-1))
+(sd(x[which(covariate.data==target.unique[2])])^2*(length(which(covariate.data==target.unique[2]))-1))/
(length(which(covariate.data==target.unique[1]))+length(which(covariate.data==target.unique[2]))-2))
})#Wei et al. BMC Genomics. 2004, 5:87
Try(exp.sd <- apply(expression.values, 1, common.sd))
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="arrow"))
########################################################
#defining if ssize or delta function to be used
##makning the menu for selecting IQR threshold
Try(ttGetPlotMethod <- tktoplevel(.affylmGUIglobals$ttMain))
Try(tkwm.deiconify(ttGetPlotMethod))
Try(tkgrab.set(ttGetPlotMethod))
Try(tkfocus(ttGetPlotMethod))
Try(tkwm.title(ttGetPlotMethod,"Sample size or Power plot"))
Try(tkgrid(tklabel(ttGetPlotMethod,text=" ")))
Try(ttGetPlotMethodTcl <- tclVar("delta"))
Try(rbSsize <- tkradiobutton(ttGetPlotMethod,text="Sample size plot",variable=ttGetPlotMethodTcl,value="ssize",font=.affylmGUIglobals$affylmGUIfont2))
Try(rbDelta<-tkradiobutton(ttGetPlotMethod,text="Power plot",variable=ttGetPlotMethodTcl,value="delta",font=.affylmGUIglobals$affylmGUIfont2))
Try(tkgrid(tklabel(ttGetPlotMethod,text=" "),rbSsize))
Try(tkgrid(tklabel(ttGetPlotMethod,text=" "),rbDelta))
Try(tkgrid.configure(rbSsize,rbDelta,columnspan=2,sticky="w"))
Try(tkgrid(tklabel(ttGetPlotMethod,text=" "),tklabel(ttGetPlotMethod,text=" ")))
Try(ReturnVal <- "")
Try(onCancel <- function() {Try(ReturnVal <<- "");Try(tkgrab.release(ttGetPlotMethod));Try(tkdestroy(ttGetPlotMethod));Try(tkfocus(.affylmGUIglobals$ttMain))})
Try(onOK <- function() {Try(ReturnVal <<- tclvalue(ttGetPlotMethodTcl));Try(tkgrab.release(ttGetPlotMethod));Try(tkdestroy(ttGetPlotMethod));Try(tkfocus(.affylmGUIglobals$ttMain))})
Try(OK.but <- tkbutton(ttGetPlotMethod,text="OK",command=onOK,font=.affylmGUIglobals$affylmGUIfont2))
Try(Cancel.but <- tkbutton(ttGetPlotMethod,text="Cancel",command=onCancel,font=.affylmGUIglobals$affylmGUIfont2))
Try(tkgrid(tklabel(ttGetPlotMethod,text=" "),OK.but,Cancel.but,tklabel(ttGetPlotMethod,text=" ")))
Try(tkgrid.configure(OK.but,sticky="e"))
Try(tkgrid.configure(Cancel.but,sticky="w"))
Try(tkgrid(tklabel(ttGetPlotMethod,text=" ")))
Try(tkbind(ttGetPlotMethod,"<Destroy>",function() {ReturnVal <- "";Try(tkgrab.release(ttGetPlotMethod));Try(tkfocus(.affylmGUIglobals$ttMain));}))
Try(tkbind(OK.but, "<Return>",onOK))
Try(tkbind(Cancel.but, "<Return>",onCancel))
Try(tkwait.window(ttGetPlotMethod))
if(ReturnVal <- ""){
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="arrow"))
Try(return())
}
#################################################################################
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="watch"))
Try(fold.change <- get("FCnum", env=affylmGUIenvironment))
Try(power <- get("Powernum", env=affylmGUIenvironment))
Try(sig.level <- get("SLnum", env=affylmGUIenvironment))
#defining the significance threshold using BH correction
Try(covariate.data <- affylmGUIenvironment$Targets$Target)
Try(target.unique <- unique(covariate.data))
if((length(which(covariate.data==target.unique[1])) + length(which(covariate.data==target.unique[2]))) == length(covariate.data)){
Try(covariate.data[which(covariate.data==target.unique[1])] <- 0)
Try(covariate.data[which(covariate.data==target.unique[2])]<- 1)
Try(covariate.data <- as.numeric(covariate.data))
Try(teststat <- mt.teststat(expression.values, covariate.data))
Try(rawp0 <- 2 * (1 - pnorm(abs(teststat))))
Try(res <- mt.rawp2adjp(rawp0, "BH"))
Try(adjp <- res$adjp)
Try(sig.level.BH <- max(adjp[which(adjp[,2] <= sig.level),1]))
####################################################################################
#pow, power.plot compute and display a cumulative plot of the fraction of
#genes achieving a specified power for a fixed sample size (n), effect size
#(delta), and significance level (sig.level).
#Try(all.power <- pow(sd = exp.sd, n = length(covariate.data), delta = log2(fold.change), sig.level = sig.level))
#Try( power.plot(all.power, lwd = 2, col = "blue")
# xmax <- par("usr")[2] - 0.05
# ymax <- par("usr")[4] - 0.05
# legend(x = xmax, y = ymax, legend = strsplit(paste("n=", n, ",","fold change=", fold.change, ",", "alpha=", sig.level, ",", "# genes=", nobs(exp.sd), sep = ""), ",")[[1]], xjust = 1, yjust = 1, cex = 1)
#)
#ssize,ssize.plot compute and display a cumulative plot of the fraction of
#genes for which a specified sample size is sufficient to achieve a specified
#power (power), effect size (delta), and significance level (sig.level).
if(ReturnVal == "ssize"){
Try(all.size <- ssize(sd = exp.sd, delta = log2(fold.change), sig.level = sig.level.BH, power = power, alpha.correct="") )
Try( ssize.plot(all.size, lwd = 2, col = "magenta", xlim = c(1, 20)))
Try( xmax <- par("usr")[2] - 1)
Try( ymin <- par("usr")[3] + 0.05 )
Try( legend(x = xmax, y = ymin, legend = strsplit(paste("fold change=", fold.change, ",", "alpha=", sig.level, ",", "power=", power, ",", "# genes=", nobs(exp.sd), sep = ""), ",")[[1]], xjust = 1, yjust = 0, cex = 1) )
Try( title(paste("Sample Size to Detect ", fold.change,"-Fold Change", collapse="")))
Try(tkmessageBox(title="Sample size plot",message="Plot is shown in the main R window", type="ok", icon="info"))
} else{
#delta,delta.plot compute and display a cumulative plot of the fraction of
#genes which can achieve a specified power (power), for a specified sample
#size (n), and significance level (sig.level) for a range of effect
#sizes.
Try(all.delta <- delta(sd = exp.sd, power = power, n = length(covariate.data)/2, sig.level = sig.level.BH, alpha.correct=""))
Try( .delta.plot1(all.delta, lwd = 2, col = "magenta", xlim = c(1, 10)) )
Try( xmax <- par("usr")[2] - 1 )
Try( ymin <- par("usr")[3] + 0.05)
Try( legend(x = xmax, y = ymin, legend = strsplit(paste("n=", length(covariate.data)/2, ",", "alpha=", sig.level, ",", "power=", power, ",", "# genes=", nobs(exp.sd), sep = ""), ",")[[1]], xjust = 1, yjust = 0, cex = 1))
Try( title(paste("Fold Change to Achieve", power * 100, "% Power", collapse=" ")))
Try(tkmessageBox(title="Power plot",message="Plot is shown in the main R window", type="ok", icon="info"))
}
} else Try(tkmessageBox(title="Sample size & Power plots",message="This analysis can be applied only to 2 group experiment\nReorganize your data to fullfil these requirements", type="ok", icon="error"))
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="arrow"))
}
#internal because siggenes overlay this function
.delta.plot1 <- function(x,
xlab="Fold Change",
ylab="Proportion of Genes",
marks=c(1.5, 2.0, 2.5, 3.0, 4.0, 6.0,10),
...)
{
n <- nobs(x)
inv <- list()
inv$x <- sort(x)
inv$y <- ecdf(x)(inv$x)
plot(inv, type="s",
xlab=xlab, ylab=ylab, yaxt="n",
..., )
vals <- pretty(inv$y * n)
labels <- paste( format(vals/n*100,digits=2), "%=", vals, sep='')
axis(side=2, at=vals/n, labels=labels, srt=90, adj=0.5)
if(!is.null(marks) && length(marks)>0 )
{
xmin <- par("usr")[1]
ymin <- par("usr")[3]
for(mark in marks)
{
y <- inv$y[ which(inv$x>mark)[1]-1 ]
lines( x=rbind( c(mark, ymin),
c(mark, y) ),
lty=2, col='red' )
text( x=mark, y=ymin, label=format(mark,2), col="red", adj=c(0,0))
lines( x=rbind( c(xmin, y),
c(mark, y) ),
lty=2, col='red' )
text( x=xmin, y=y,
label=paste(format(y*100,digits=2),"%=",
format(y*n,digits=2), sep=''),
col="red", adj=c(0,0), xpd=TRUE)
}
}
}
################################################################################
#part of the functions used to evaluate sample size and statistical power estimation sizepower package
# sd distribution
"sample.size.evaluation1" <- function(){
# require(sizepower) || stop("library sizepower could not be found !")
#error if no data are loaded
Try(whichArrayPlatform <- get("whichArrayPlatform",envir=affylmGUIenvironment))
if(whichArrayPlatform ==""){
Try(tkmessageBox(title="Study design",message="No arrays have been loaded. Please try New or Open from the File menu.",type="ok",icon="error"))
Try(tkfocus(.affylmGUIglobals$ttMain))
Try(return())
}
#########################
if(whichArrayPlatform =="EXON"){
Try(NormalizedAffyData <- get("NormalizedAffyData", env=affylmGUIenvironment))
}else{
if(affylmGUIenvironment$NormalizedAffyData.Available){
Try(NormalizedAffyData <- get("NormalizedAffyData", env=affylmGUIenvironment))
} else {
Try(tkmessageBox(title="Sample size & Power Experiment Estimation",message="Normalized data are not available.\n Please calculate the probe set expression summaries ", type="ok", icon="error"))
Try(return())
}
}
Try(expression.values <- exprs(NormalizedAffyData))
covariate.data <- affylmGUIenvironment$Targets$Target
target.unique <- unique(covariate.data)
if(length(target.unique)>2){
Try(tkmessageBox(title="Sample size & Power Experiment Estimation",message="This function apply only two class experiment.", type="ok", icon="error"))
return()
} else{
##Selecting the function to be used
Try(ttsizepowerMethod <- tktoplevel(.affylmGUIglobals$ttMain))
Try(tkwm.deiconify(ttsizepowerMethod))
Try(tkgrab.set(ttsizepowerMethod))
Try(tkfocus(ttsizepowerMethod))
Try(tkwm.title(ttsizepowerMethod,"Sample size & Power Experiment Estimation"))
Try(tkgrid(tklabel(ttsizepowerMethod,text=" ")))
Try(ttsizepowerMethodTcl <- tclVar("size"))
Try(rbSsize <- tkradiobutton(ttsizepowerMethod,text="Sample size estimation",variable=ttsizepowerMethodTcl,value="size",font=.affylmGUIglobals$affylmGUIfont2))
Try(rbPower<-tkradiobutton(ttsizepowerMethod,text="Power estimation",variable=ttsizepowerMethodTcl,value="power",font=.affylmGUIglobals$affylmGUIfont2))
Try(tkgrid(tklabel(ttsizepowerMethod,text=" "),rbSsize))
Try(tkgrid(tklabel(ttsizepowerMethod,text=" "),rbPower))
Try(tkgrid.configure(rbSsize,rbPower,columnspan=2,sticky="w"))
Try(tkgrid(tklabel(ttsizepowerMethod,text=" "),tklabel(ttsizepowerMethod,text=" ")))
Try(ReturnVal <- "")
Try(onCancel <- function() {Try(ReturnVal <<- "");Try(tkgrab.release(ttsizepowerMethod));Try(tkdestroy(ttsizepowerMethod));Try(tkfocus(.affylmGUIglobals$ttMain))})
Try(onOK <- function() {Try(ReturnVal <<- tclvalue(ttsizepowerMethodTcl));Try(tkgrab.release(ttsizepowerMethod));Try(tkdestroy(ttsizepowerMethod));Try(tkfocus(.affylmGUIglobals$ttMain))})
Try(OK.but <- tkbutton(ttsizepowerMethod,text="OK",command=onOK,font=.affylmGUIglobals$affylmGUIfont2))
Try(Cancel.but <- tkbutton(ttsizepowerMethod,text="Cancel",command=onCancel,font=.affylmGUIglobals$affylmGUIfont2))
Try(tkgrid(tklabel(ttsizepowerMethod,text=" "),OK.but,Cancel.but,tklabel(ttsizepowerMethod,text=" ")))
Try(tkgrid.configure(OK.but,sticky="e"))
Try(tkgrid.configure(Cancel.but,sticky="w"))
Try(tkgrid(tklabel(ttsizepowerMethod,text=" ")))
Try(tkbind(ttsizepowerMethod,"<Destroy>",function() {ReturnVal <- "";Try(tkgrab.release(ttsizepowerMethod));Try(tkfocus(.affylmGUIglobals$ttMain));}))
Try(tkbind(OK.but, "<Return>",onOK))
Try(tkbind(Cancel.but, "<Return>",onCancel))
Try(tkwait.window(ttsizepowerMethod))
#######################################################Ã Ã
if(ReturnVal == ""){
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="arrow"))
Try(return())
}
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="watch"))
Try(common.sd<-function(x){
covariate.data <<- affylmGUIenvironment$Targets$Target
target.unique <- unique(covariate.data)
common.sd1<- sqrt((sd(x[which(covariate.data==target.unique[1])])^2*(length(which(covariate.data==target.unique[1]))-1))
+(sd(x[which(covariate.data==target.unique[2])])^2*(length(which(covariate.data==target.unique[2]))-1))/
(length(which(covariate.data==target.unique[1]))+length(which(covariate.data==target.unique[2]))-2))
})#Wei et al. BMC Genomics. 2004, 5:87
Try(exp.sd <- apply(expression.values, 1, common.sd))
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="arrow"))
########################################################
Try(if(ReturnVal=="size"){
# Try(tkmessageBox(title="Sample sixe evaluation",message="This routine computes the required sample size.",type="ok",icon="info"))
##making the menu for selecting sample sixe parameters
Try(ttsizepowerDialog<-tktoplevel(.affylmGUIglobals$ttMain))
Try(tkwm.deiconify(ttsizepowerDialog))
Try(tkgrab.set(ttsizepowerDialog))
Try(tkfocus(ttsizepowerDialog))
Try(tkwm.title(ttsizepowerDialog,"Sample size parameters"))
Try(tkgrid(tklabel(ttsizepowerDialog,text=" ")))
#Try(frame1 <- tkframe(ttsizepowerDialog,relief="groove",borderwidth=2))
#Try(HowManyQuestion1 <- tklabel(frame1,text="Mean number of false positives",font=.affylmGUIglobals$affylmGUIfont2))
#Try(tkgrid(HowManyQuestion1))
#Try(tkgrid.configure(HowManyQuestion1,columnspan=2,sticky="w"))
Try(fTcl <- tclVar("1"))
#Try(f1.but <- tkradiobutton(frame1,text="1",variable=fTcl,value=1,font=.affylmGUIglobals$affylmGUIfont2))
#Try(f2.but <- tkradiobutton(frame1,text="5",variable=fTcl,value=5,font=.affylmGUIglobals$affylmGUIfont2))
#Try(f3.but <- tkradiobutton(frame1,text="10",variable=fTcl,value=10,font=.affylmGUIglobals$affylmGUIfont2))
#Try(f4.but <- tkradiobutton(frame1,text="20",variable=fTcl,value=20,font=.affylmGUIglobals$affylmGUIfont2))
#Try(f5.but <- tkradiobutton(frame1,text="40",variable=fTcl,value=40,font=.affylmGUIglobals$affylmGUIfont2))
#Try(tkgrid(f1.but,sticky="w"))
#Try(tkgrid(f2.but,sticky="w"))
#Try(tkgrid(f3.but,sticky="w"))
#Try(tkgrid(f4.but,sticky="w"))
#Try(tkgrid(f5.but,sticky="w"))
#Try(tkgrid.configure(HowManyQuestion1,f1.but,f2.but,f3.but,f4.but,f5.but,sticky="w"))
Try(frame2 <- tkframe(ttsizepowerDialog,relief="groove",borderwidth=2))
Try(powerLabel <- tklabel(frame2,text="Power level for an individual gene",font=.affylmGUIglobals$affylmGUIfont2))
Try(tkgrid(powerLabel,sticky="w"))
Try(tkgrid.configure(powerLabel,sticky="w"))
Try(powerTcl <- tclVar("0.9"))
Try(p1.but <- tkradiobutton(frame2,text="0.99",variable=powerTcl,value=0.99,font=.affylmGUIglobals$affylmGUIfont2))
Try(p2.but <- tkradiobutton(frame2,text="0.95",variable=powerTcl,value=0.95,font=.affylmGUIglobals$affylmGUIfont2))
Try(p3.but <- tkradiobutton(frame2,text="0.9",variable=powerTcl,value=0.9,font=.affylmGUIglobals$affylmGUIfont2))
Try(p4.but <- tkradiobutton(frame2,text="0.85",variable=powerTcl,value=0.85,font=.affylmGUIglobals$affylmGUIfont2))
Try(p5.but <- tkradiobutton(frame2,text="0.8",variable=powerTcl,value=0.8,font=.affylmGUIglobals$affylmGUIfont2))
Try(tkgrid(p1.but,sticky="w"))
Try(tkgrid(p2.but,sticky="w"))
Try(tkgrid(p3.but,sticky="w"))
Try(tkgrid(p4.but,sticky="w"))
Try(tkgrid(p5.but,sticky="w"))
Try(frame3 <- tkframe(ttsizepowerDialog,relief="groove",borderwidth=2))
Try(fcLabel <- tklabel(frame3,text="Absolute log2(Fold Change)",font=.affylmGUIglobals$affylmGUIfont2))
Try(tkgrid(fcLabel,sticky="w"))
Try(tkgrid.configure(fcLabel,sticky="w"))
Try(fcTcl <- tclVar("1"))
Try(fc1.but <- tkradiobutton(frame3,text="1",variable=fcTcl,value=1,font=.affylmGUIglobals$affylmGUIfont2))
Try(fc2.but <- tkradiobutton(frame3,text="1.5" ,variable=fcTcl,value=1.5 ,font=.affylmGUIglobals$affylmGUIfont2))
Try(fc3.but <- tkradiobutton(frame3,text="2" ,variable=fcTcl,value=2 ,font=.affylmGUIglobals$affylmGUIfont2))
Try(fc4.but <- tkradiobutton(frame3,text="2.5",variable=fcTcl,value=2.5,font=.affylmGUIglobals$affylmGUIfont2))
Try(tkgrid(fc1.but,sticky="w"))
Try(tkgrid(fc2.but ,sticky="w"))
Try(tkgrid(fc3.but ,sticky="w"))
Try(tkgrid(fc4.but,sticky="w"))
Try(Abort <- 1)
sizepower.param <- list()
Try(onOK <- function()
{
Try(sizepower.param[[1]] <<- tclvalue(fTcl))
Try(tkgrab.release(ttsizepowerDialog))
Try(tkdestroy(ttsizepowerDialog))
Try(tkfocus(.affylmGUIglobals$ttMain))
Try(sizepower.param[[2]] <<- tclvalue(powerTcl))
Try(sizepower.param[[3]] <<- tclvalue(fcTcl))
Try(Abort <<- 0)
})
#Try(onHelp <- function() Try(help("topTable",htmlhelp=TRUE)))
Try(frame4 <- tkframe(ttsizepowerDialog,borderwidth=2))
Try(onCancel <- function() {Try(tkgrab.release(ttsizepowerDialog));Try(tkdestroy(ttsizepowerDialog));Try(tkfocus(.affylmGUIglobals$ttMain));Abort <<- 1})
Try(OK.but <-tkbutton(frame4,text=" OK ",command=onOK,font=.affylmGUIglobals$affylmGUIfont2))
Try(Cancel.but <-tkbutton(frame4,text=" Cancel ",command=onCancel,font=.affylmGUIglobals$affylmGUIfont2))
#Try(Help.but <-tkbutton(frame4,text=" Help ",command=onHelp,font=.affylmGUIglobals$affylmGUIfont2))
Try(tkgrid(tklabel(frame4,text=" "),OK.but,Cancel.but,tklabel(frame4,text=" ")))
Try(tkgrid(tklabel(ttsizepowerDialog,text=" "),frame2,tklabel(ttsizepowerDialog,text=" ")))
#Try(tkgrid(tklabel(ttsizepowerDialog,text=" ")))
Try(tkgrid(tklabel(ttsizepowerDialog,text=" "),frame3,frame4,tklabel(ttsizepowerDialog,text=" ")))
#Try(tkgrid(tklabel(ttsizepowerProDialog,text=" ")))
Try(tkgrid.configure(frame2, frame3,sticky="w"))
#Try(tkgrid.configure(frame1,frame3,sticky="w"))
# Try(tkgrid.configure(frame4,sticky="s"))
Try(tkfocus(ttsizepowerDialog))
Try(tkbind(ttsizepowerDialog, "<Destroy>", function() {Try(tkgrab.release(ttsizepowerDialog));Try(tkfocus(.affylmGUIglobals$ttMain));}))
Try(tkwait.window(ttsizepowerDialog))
Try(if(Abort==1) return())
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="watch"))
#In this case the sample size is based on the mean of the common variance
Try(mysample <- sampleSize.randomized(ER0 = as.numeric(sizepower.param[[1]]),
G0 = dim(expression.values)[1],
power = as.numeric(sizepower.param[[2]]),
absMu1 = as.numeric(sizepower.param[[3]]),
sigmad = sqrt(2)*mean(exp.sd))
)
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="arrow"))
Try(tkmessageBox(title="Sample size evaluation",message=paste("Given a",sizepower.param[[1]],"mean number of false positives\n",sizepower.param[[2]],"power\n",sizepower.param[[3]],"absolute mean difference in log-expression between treatment and control\n","The sample size (per group) is",mysample$n, sep=" "),type="ok",icon="info"))
Try(cat(paste("Sample size evaluation:\n","Given a",sizepower.param[[1]],"mean number of false positives\n",sizepower.param[[2]],"power\n",sizepower.param[[3]],"absolute mean difference in log-expression between treatment and control\n","The sample size (per group) is",mysample$n,"\n", sep=" ")))
} else {
# Try(tkmessageBox(title="Power evaluation",message="This routine computes the individual \npower value for a completely randomized design.\n This power value is the expected fraction of truly differentially expressed genes that \nwill be correctly declared as differentially expressed by the tests.",type="ok",icon="info"))
##making the menu for selecting the power parameters
Try(ttsizepowerDialog<-tktoplevel(.affylmGUIglobals$ttMain))
Try(tkwm.deiconify(ttsizepowerDialog))
Try(tkgrab.set(ttsizepowerDialog))
Try(tkfocus(ttsizepowerDialog))
Try(tkwm.title(ttsizepowerDialog,"Sample size parameters"))
Try(tkgrid(tklabel(ttsizepowerDialog,text=" ")))
#Try(frame1 <- tkframe(ttsizepowerDialog,relief="groove",borderwidth=2))
#Try(HowManyQuestion1 <- tklabel(frame1,text=
# "Mean number of false positives",font=.affylmGUIglobals$affylmGUIfont2))
#Try(tkgrid(HowManyQuestion1))
#Try(tkgrid.configure(HowManyQuestion1,columnspan=2,sticky="w"))
Try(fTcl <- tclVar("1"))
#Try(f1.but <- tkradiobutton(frame1,text="1",variable=fTcl,value=1,font=.affylmGUIglobals$affylmGUIfont2))
#Try(f2.but <- tkradiobutton(frame1,text="5",variable=fTcl,value=5,font=.affylmGUIglobals$affylmGUIfont2))
#Try(f3.but <- tkradiobutton(frame1,text="10",variable=fTcl,value=10,font=.affylmGUIglobals$affylmGUIfont2))
#Try(f4.but <- tkradiobutton(frame1,text="20",variable=fTcl,value=20,font=.affylmGUIglobals$affylmGUIfont2))
#Try(f5.but <- tkradiobutton(frame1,text="40",variable=fTcl,value=40,font=.affylmGUIglobals$affylmGUIfont2))
#Try(tkgrid(f1.but,sticky="w"))
#Try(tkgrid(f2.but,sticky="w"))
#Try(tkgrid(f3.but,sticky="w"))
#Try(tkgrid(f4.but,sticky="w"))
#Try(tkgrid(f5.but,sticky="w"))
#Try(tkgrid.configure(HowManyQuestion1,f1.but,f2.but,f3.but,f4.but,f5.but,sticky="w"))
Try(frame2 <- tkframe(ttsizepowerDialog,relief="groove",borderwidth=2))
Try(fcLabel <- tklabel(frame2,text="Absolute log2(Fold Change)",font=.affylmGUIglobals$affylmGUIfont2))
Try(tkgrid(fcLabel,sticky="w"))
Try(tkgrid.configure(fcLabel,sticky="w"))
Try(fcTcl <- tclVar("1"))
Try(fc1.but <- tkradiobutton(frame2,text="1",variable=fcTcl,value=1,font=.affylmGUIglobals$affylmGUIfont2))
Try(fc2.but <- tkradiobutton(frame2,text="1.5" ,variable=fcTcl,value=1.5 ,font=.affylmGUIglobals$affylmGUIfont2))
Try(fc3.but <- tkradiobutton(frame2,text="2" ,variable=fcTcl,value=2 ,font=.affylmGUIglobals$affylmGUIfont2))
Try(fc4.but <- tkradiobutton(frame2,text="2.5",variable=fcTcl,value=2.5,font=.affylmGUIglobals$affylmGUIfont2))
Try(tkgrid(fc1.but,sticky="w"))
Try(tkgrid(fc2.but ,sticky="w"))
Try(tkgrid(fc3.but ,sticky="w"))
Try(tkgrid(fc4.but,sticky="w"))
Try(Abort <- 1)
sizepower.param <- list()
Try(onOK <- function()
{
Try(sizepower.param[[1]] <<- tclvalue(fTcl))
Try(tkgrab.release(ttsizepowerDialog))
Try(tkdestroy(ttsizepowerDialog))
Try(tkfocus(.affylmGUIglobals$ttMain))
Try(sizepower.param[[2]] <<- tclvalue(fcTcl))
Try(Abort <<- 0)
})
#Try(onHelp <- function() Try(help("topTable",htmlhelp=TRUE)))
Try(frame3 <- tkframe(ttsizepowerDialog,borderwidth=2))
Try(onCancel <- function() {Try(tkgrab.release(ttsizepowerDialog));Try(tkdestroy(ttsizepowerDialog));Try(tkfocus(.affylmGUIglobals$ttMain));Abort <<- 1})
Try(OK.but <-tkbutton(frame3,text=" OK ",command=onOK,font=.affylmGUIglobals$affylmGUIfont2))
Try(Cancel.but <-tkbutton(frame3,text=" Cancel ",command=onCancel,font=.affylmGUIglobals$affylmGUIfont2))
#Try(Help.but <-tkbutton(frame4,text=" Help ",command=onHelp,font=.affylmGUIglobals$affylmGUIfont2))
Try(tkgrid(tklabel(frame3,text=" "),OK.but,Cancel.but,tklabel(frame3,text=" ")))
Try(tkgrid(tklabel(ttsizepowerDialog,text=" "),frame2,tklabel(ttsizepowerDialog,text=" ")))
#Try(tkgrid(tklabel(ttsizepowerDialog,text=" ")))
Try(tkgrid(tklabel(ttsizepowerDialog,text=" "),frame3,tklabel(ttsizepowerDialog,text=" ")))
#Try(tkgrid(tklabel(ttsizepowerProDialog,text=" ")))
Try(tkgrid.configure(frame2,frame3,sticky="w"))
# Try(tkgrid.configure(frame4,sticky="s"))
Try(tkfocus(ttsizepowerDialog))
Try(tkbind(ttsizepowerDialog, "<Destroy>", function() {Try(tkgrab.release(ttsizepowerDialog));Try(tkfocus(.affylmGUIglobals$ttMain));}))
Try(tkwait.window(ttsizepowerDialog))
Try(if(Abort==1) return())
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="watch"))
#In this case the sample size is based on the mean of the common variance
Try(mysample <- power.randomized(ER0 = as.numeric(sizepower.param[[1]]),
G0 = dim(expression.values)[1],
absMu1 = as.numeric(sizepower.param[[2]]),
sigmad = sqrt(2)*mean(exp.sd),
n=ceiling(dim(expression.values)[2]/2))
)
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="arrow"))
Try(tkmessageBox(title="Power evaluation",message=paste("Given a",sizepower.param[[1]],"mean number of false positives\n",(dim(expression.values)[2]/2),"replicates for each condition\n",sizepower.param[[2]]," absolute mean difference in log-expression between treatment and control\n","the power is",signif(mysample$power,2), sep=" "),type="ok",icon="info"))
Try(cat(paste("Power evaluation","Given a",sizepower.param[[1]],"mean number of false positives\n",(dim(expression.values)[2]/2),"replicates for each condition\n",sizepower.param[[2]]," absolute mean difference in log-expression between treatment and control\n","the power is",signif(mysample$power,2),"\n", sep=" ")))
})
}
}
################################################################################
PlotOptionsv1 <- function()
{
Try(ttGetPlotOptions<-tktoplevel(.affylmGUIglobals$ttMain))
Try(tkwm.title(ttGetPlotOptions,"Plot Options"))
Try(tkwm.deiconify(ttGetPlotOptions))
Try(tkgrab.set(ttGetPlotOptions))
Try(tkframe1 <- tkframe(ttGetPlotOptions,borderwidth=2))
Try(tkframe2 <- tkframe(tkframe1,relief="groove",borderwidth=2))
Try(tkframe4<-tkframe(tkframe1,borderwidth=2))
Try(tkgrid(tklabel(tkframe1,text=" ")))
Try(tkgrid(tklabel(tkframe2,text="Choose a graphics device for plotting.",font=.affylmGUIglobals$affylmGUIfont2),column=2,rowspan=1,columnspan=2,sticky="w"))
Try(affylmGUIglobals <- get(".affylmGUIglobals",envir=.GlobalEnv))
Try(if (!("graphicsDevice" %in% names(affylmGUIglobals)))
{
Try(affylmGUIglobals$graphicsDevice <- "R")
Try(assign(".affylmGUIglobals",affylmGUIglobals,.GlobalEnv))
})
#Try(graphicsDevice <- .affylmGUIglobals$graphicsDevice)
Try(graphicsDevice <- "R")
Try(graphicsDeviceTcl <- tclVar(graphicsDevice))
Try(tkrplot.but <- tkradiobutton(tkframe2,text="Tk R Plot",variable=graphicsDeviceTcl,value="tkrplot",font=.affylmGUIglobals$affylmGUIfont2))
Try(R.but <- tkradiobutton(tkframe2,text="R",variable=graphicsDeviceTcl,value="R",font=.affylmGUIglobals$affylmGUIfont2))
Try(tkgrid(tkrplot.but,column=2))
Try(tkgrid(R.but,column=2))
Try(tkgrid.configure(tkrplot.but,R.but,sticky="w"))
Try(tkgrid(tkframe2))
Try(newGraphicsDevice <- "")
onOK <- function()
{
Try(newGraphicsDevice<<-tclvalue(graphicsDeviceTcl))
Try(tkgrab.release(ttGetPlotOptions))
Try(tkdestroy(ttGetPlotOptions))
Try(if (newGraphicsDevice==graphicsDevice)
return())
Try(graphicsDevice <- newGraphicsDevice)
Try(if (graphicsDevice=="R" && .Platform$OS.type=="windows")
Try(tkmessageBox(title="R graphics device",
message="It is strongly recommended that you run R in SDI (Single Document Interface) mode when using the R graphics device",icon="warning")))
Try(affylmGUIglobals <- get(".affylmGUIglobals",envir=.GlobalEnv))
Try(affylmGUIglobals$graphicsDevice <- graphicsDevice)
Try(assign(".affylmGUIglobals",affylmGUIglobals,.GlobalEnv))
Try(tkfocus(.affylmGUIglobals$ttMain))
}
Try(OK.but <-tkbutton(tkframe4,text=" OK ",command=onOK,font=.affylmGUIglobals$affylmGUIfont2))
Try(Cancel.but <-tkbutton(tkframe4,text=" Cancel ",command=function(){Try(tkgrab.release(ttGetPlotOptions));Try(tkdestroy(ttGetPlotOptions));newGraphicsDevice<-"";Try(tkfocus(.affylmGUIglobals$ttMain))},font=.affylmGUIglobals$affylmGUIfont2))
Try(onHelp <- function() tkmessageBox(title="Plotting Device",
message="The R graphics is device can be resized more easily, but it may be inconvenient for Windows users running R in MDI mode.",
icon="info"))
Try(Help.but <- tkbutton(tkframe4,text=" Help ",command=function()Try(onHelp()),font=.affylmGUIglobals$affylmGUIfont2))
Try(tkgrid(tklabel(tkframe4,text=" ")))
Try(tkgrid(OK.but,Cancel.but,Help.but))
Try(tkgrid.configure(OK.but,sticky="e"))
Try(tkgrid.configure(Cancel.but,sticky="e"))
Try(tkgrid.configure(Help.but,sticky="e"))
Try(tkgrid(tklabel(tkframe4,text=" ")))
Try(tkgrid(tkframe4))
Try(tkgrid(tkframe1))
Try(tkfocus(OK.but))
Try(tkbind(ttGetPlotOptions, "<Return>",onOK))
Try(tkbind(ttGetPlotOptions, "<Destroy>", function() {Try(tkgrab.release(ttGetPlotOptions));Try(tkfocus(.affylmGUIglobals$ttMain))}))
Try(tkwait.window(ttGetPlotOptions))
Try(tkdestroy(ttGetPlotOptions))
# This return value below is not used. The function above is used for its effect
# on PlotOptions in affylmGUIenvironment
return(newGraphicsDevice)
}
################################################################################
affyPlotMA <- function(){
Try(ArraysLoaded <- get("ArraysLoaded", envir=affylmGUIenvironment))
Try(SlideNamesVec <- get("SlideNamesVec", envir=affylmGUIenvironment))
Try(RawAffyData <- get("RawAffyData",envir=affylmGUIenvironment))
Try(
if (ArraysLoaded==FALSE){
Try(tkmessageBox(title="M A Plot",message="Error: No arrays have been loaded.", icon="error",default="ok"))
return()
}
)
Try(LocalHScale <- .affylmGUIglobals$Myhscale)
Try(LocalVScale <- .affylmGUIglobals$Myvscale)
#
Try(SlideNums <- GetSlideNums())
Try(if (length(SlideNums)==0) return())
Try(slide1 <- SlideNums$slide1)
Try(slide2 <- SlideNums$slide2)
#
Try(WhetherToNormalize <- tclvalue(tkmessageBox(title="M A Plot",message="Use normalized data?",type="yesnocancel",icon="question")))
Try(if (WhetherToNormalize=="cancel") return())
#
Try(
if (WhetherToNormalize=="yes"){
Try(NormalizedAffyData.Available <- get("NormalizedAffyData.Available",envir=affylmGUIenvironment))
Try(
if (NormalizedAffyData.Available==FALSE){
NormalizeNow()
}
)
Try(NormalizedAffyData.Available <- get("NormalizedAffyData.Available",envir=affylmGUIenvironment))
Try(
if (NormalizedAffyData.Available==FALSE){
tkmessageBox(title="M A Plot",message="An error occured while trying to normalize the data.")
return()
}
)
Try(NormalizedAffyData <- get("NormalizedAffyData", envir=affylmGUIenvironment))
Try(NormalizedAffyData.exprs <- exprs(NormalizedAffyData))
Try(R <- NormalizedAffyData.exprs[,slide1]) # Using cDNA notation (R for one channel/array, G for the other)
Try(G <- NormalizedAffyData.exprs[,slide2]) # Using cDNA notation (R for one channel/array, G for the other)
pch <- 16
cex <- 0.2
}else{
Try(R <- log2(exprs(RawAffyData)[,slide1])) # Using cDNA notation (R for one channel/array, G for the other)
Try(G <- log2(exprs(RawAffyData)[,slide2])) # Using cDNA notation (R for one channel/array, G for the other)
pch <- "."
cex <- 1
}
)
# R and G are already log2ed.
M <- R - G
A <- 0.5*(R+G)
Try(
plotFunction <- function(){
Try(opar<-par(bg="white"))
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="watch"))
Try(plot(A,M,pch=pch,cex=cex,xlab=xLabel,ylab=yLabel))
Try(title(plotTitle))
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="arrow"))
Try(tmp<-par(opar))
}#end of plotFunction <- function()
)
Try(
if (WhetherToNormalize=="yes"){
Try(plotTitle<-paste("Normalized M A Plot (",SlideNamesVec[slide1]," vs ",SlideNamesVec[slide2],")",sep=""))
}else{
Try(plotTitle<-paste("Raw M A Plot (",SlideNamesVec[slide1]," vs ",SlideNamesVec[slide2],")",sep=""))
}
)
Try(plotLabels <- GetPlotLabels(plotTitle,"A","M"))
Try(if (length(plotLabels)==0) return())
Try(plotTitle <- plotLabels$plotTitle)
Try(xLabel <- plotLabels$xLabel)
Try(yLabel <- plotLabels$yLabel)
#
Try(
if(.affylmGUIglobals$graphicsDevice=="tkrplot"){
# require("tkrplot")
CopyToClip <- function() Try(tkrreplot(imgaffylmGUI))
Try(ttGraph<-tktoplevel(.affylmGUIglobals$ttMain))
Try(tkwm.withdraw(ttGraph))
Try(tkwm.title(ttGraph,plotTitle))
Try(imgaffylmGUI<-tkrplot(ttGraph,plotFunction,hscale=LocalHScale,vscale=LocalVScale))
Try(tkwm.title(ttGraph,plotTitle))
SetupPlotKeyBindings(tt=ttGraph,img=imgaffylmGUI)
SetupPlotMenus(tt=ttGraph,initialfile="",plotFunction,img=imgaffylmGUI)
Try(tkgrid(imgaffylmGUI))
Try(
if(as.numeric(tclvalue(tkwinfo("reqheight",imgaffylmGUI)))<10){ # Nothing plotted.
Try(tkdestroy(ttGraph))
}else{
Try(tkwm.deiconify(ttGraph))
Try(tkfocus(imgaffylmGUI))
}
)
}else{
Try(plot.new())
Try(plotFunction())
}
)
}#end of affyPlotMA <- function()
################################################################################
"rawBoxplotPN" <- function(){
#error if no data are loaded
Try(whichArrayPlatform <- get("whichArrayPlatform",envir=affylmGUIenvironment))
if(whichArrayPlatform ==""){
Try(tkmessageBox(title="QC",message="No arrays have been loaded. Please try New or Open from the File menu.",type="ok",icon="error"))
Try(tkfocus(.affylmGUIglobals$ttMain))
Try(return())
}
if(whichArrayPlatform!="EXON"){return()} #only on exons
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="watch"))
Try(localDir <- getwd())
Try(whichLib <- get("whichLib", affylmGUIenvironment))
Try(affylibs <- dir(system.file("affylibs",package="oneChannelGUI")))
Try(ctrl <- affylibs[intersect(grep(whichLib[[1]][1], affylibs), grep("controls", affylibs))])
#check if the affylibs are available else it install it
Try(if(length(ctrl) == 0){
tkmessageBox(title="QC",message="It seems that the Affymetrix/Apt libraries are not available.\nNext messages will help you to install/set them.",type="ok",icon="error")
aptFolder()
geneExonLibs()
})
Try(ctrl.table <- read.table(paste(system.file("affylibs",package="oneChannelGUI"),"/",ctrl, sep=""), sep="\t", as.is=T, header=T))
Try(pgf <- paste(system.file("affylibs",package="oneChannelGUI"),"/",affylibs[intersect(grep(whichLib[[1]][1], affylibs), grep("pgf", affylibs))],sep=""))
Try(clf <- paste(system.file("affylibs",package="oneChannelGUI"),"/",affylibs[intersect(grep(whichLib[[1]][1], affylibs), grep("clf", affylibs))],sep=""))
setwd(localDir)
Try(p.ctrl <- ctrl.table[which(ctrl.table[,2]=="pos_control"),])
Try(n.ctrl <- ctrl.table[which(ctrl.table[,2]=="neg_control"),])
Try(pn.ctrl <- rbind(p.ctrl, n.ctrl))
Try(write.table(pn.ctrl, "ctrlpn.txt", sep="\t", row.names=F))
#defining the temp file containing target info for apt extract
Try(Targets <- get("Targets",envir=affylmGUIenvironment))
Try(tempTarget <- tempfile(pattern = "target", tmpdir = getwd()))
Try(tempTarget <- sub( "\\\\","/",tempTarget)) #changing double backslach with slash
Try(write.table(Targets[,2:3], tempTarget, sep="\t", row.names =F, col.names = c("cel_files", "group_id")))
Try(tempOut <- tempfile(pattern = "out", tmpdir = getwd()))#creating a temp outfile
Try(tempOut <- sub( "\\\\","/",tempOut)) #changing double backslach with slash
#running apt-cel-extract
Try(extractCel <- paste(get("aptDir", affylmGUIenvironment),"/bin/apt-cel-extract", sep=""))
Try(extractCel <- paste(extractCel, " -o rawPN.txt ", "-p ", pgf ," -c ",clf," --probeset-ids ctrlpn.txt ", "--cel-files " , tempTarget, sep=""))
Try(cat("Be patient...... starting probe signal extraction ...."))
Try(system(extractCel))
Try(cat("Be patient...... ending probe signal extraction ...."))
#creating the box plot fro P and N
Try(tmp <- read.table("rawPN.txt", sep="\t", header=T))
Try(tmp.p <- tmp[which(tmp$probeset_id%in%p.ctrl$probeset_id), 8:dim(tmp)[2]])
Try(names(tmp.p) <- Targets$Name)
Try(tmp.p <- log2(tmp.p))
Try(tmp.n <- tmp[which(tmp$probeset_id%in%n.ctrl$probeset_id), 8:dim(tmp)[2]])
Try(names(tmp.n) <- Targets$Name)
Try(tmp.n <- log2(tmp.n))
Try(par(mfrow=c(1,2)))
Try(boxplot(tmp.p, main="Positive Ctrls", ylab="raw log2(intensity)", las=2))
Try(boxplot(tmp.n, main="Negative Ctrls", ylab="raw log2(intensity)", las=2))
Try(tkmessageBox(title="Raw probes intensities from CELs",message="Box plot of raw controls intensity data is available in main R window",icon="info"))
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="arrow"))
}
################################################################################
"qcMDS" <- function(){
# Try(require(edgeR) || stop("Missing edgeR library"))
Try(Targets <- get("Targets",envir=affylmGUIenvironment))
Try(whichArrayPlatform <- get("whichArrayPlatform",envir=affylmGUIenvironment))
if(whichArrayPlatform ==""){
Try(tkmessageBox(title="QC",message="No arrays have been loaded. Please try New or Open from the File menu.",type="ok",icon="error"))
Try(tkfocus(.affylmGUIglobals$ttMain))
Try(return())
}
if(affylmGUIenvironment$NormalizedAffyData.Available & affylmGUIenvironment$NGS.Available){
Try(NormalizedAffyData <- get("NormalizedAffyData", env=affylmGUIenvironment))
Try(mappedReads <- get("mappedReads", env=affylmGUIenvironment))
Try(targets <- get("Targets", env=affylmGUIenvironment))
} else Try(tkmessageBox(title="NGS data set",message="Normalized data are not available.", type="ok", icon="error"))
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="watch"))
cat("\ncreating the DGEList")
Try(NGSscaling.Available <- get("NGSscaling.Available", env=affylmGUIenvironment))
if(NGSscaling.Available){
Try(scaledReads <- get("NGSscaling", env=affylmGUIenvironment))
Try(mylist <- DGEList(counts= exprs(NormalizedAffyData), group=as.factor(targets$Target), lib.size=scaledReads))
} else {Try(mylist <- DGEList(counts= exprs(NormalizedAffyData), group=as.factor(targets$Target)))}
Try(mylist <- estimateCommonDisp(mylist))
Try(plotMDS.DGEList(mylist, labels=Targets$Name, main=paste("Multidimensional scaling plot\nCommon disp. after normalization",signif(mylist$common.dispersion,2),sep=" ")))
Try(tkmessageBox(title="Multdimensional scaling plot",message="Multidimensional scaling plot is available in main R window",icon="info"))
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="arrow"))
}
################################################################################
"EDAplotQuality" <- function(){
# require(EDASeq) || stop("Missing EDASeq library")
Try(whichArrayPlatform <- get("whichArrayPlatform",envir=affylmGUIenvironment))
if(whichArrayPlatform ==""){
Try(tkmessageBox(title="QC",message="No arrays have been loaded. Please try New or Open from the File menu.",type="ok",icon="error"))
Try(tkfocus(.affylmGUIglobals$ttMain))
Try(return())
}
if(affylmGUIenvironment$NormalizedAffyData.Available & affylmGUIenvironment$NGS.Available){
Try(NormalizedAffyData <- get("NormalizedAffyData", env=affylmGUIenvironment))
Try(targets <- get("Targets", env=affylmGUIenvironment))
} else Try(tkmessageBox(title="NGS data set",message="Normalized data are not available.", type="ok", icon="error"))
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="watch"))
Try(bfs <- BamFileList(targets$FileName))
Try(pd <- DataFrame("name"=targets$Name, "Target"= targets$Target, row.names=paste(targets$Name, targets$Target, sep=".")))
Try(elementMetadata(bfs) <- pd)
Try(plotQuality(bfs))
Try(legend("topright",unique(elementMetadata(bfs)[,1]),fill=rainbow(length(unique(elementMetadata(bfs)[,1])))))
Try(tkmessageBox(title="EDASeq Quality plot",message="EDASeq Quality plot is available in main R window",icon="info"))
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="arrow"))
}
################################################################################
"EDAreadNumber" <- function(){
# require(EDASeq) || stop("Missing EDASeq library")
Try(whichArrayPlatform <- get("whichArrayPlatform",envir=affylmGUIenvironment))
if(whichArrayPlatform ==""){
Try(tkmessageBox(title="QC",message="No arrays have been loaded. Please try New or Open from the File menu.",type="ok",icon="error"))
Try(tkfocus(.affylmGUIglobals$ttMain))
Try(return())
}
if(affylmGUIenvironment$NormalizedAffyData.Available & affylmGUIenvironment$NGS.Available){
Try(NormalizedAffyData <- get("NormalizedAffyData", env=affylmGUIenvironment))
Try(targets <- get("Targets", env=affylmGUIenvironment))
} else Try(tkmessageBox(title="NGS data set",message="Normalized data are not available.", type="ok", icon="error"))
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="watch"))
Try(bfs <- BamFileList(targets$FileName))
Try(pd <- DataFrame("name"=targets$Name, "Target"= targets$Target, row.names=paste(targets$Name, targets$Target, sep=".")))
Try(elementMetadata(bfs) <- pd)
Try(barplot(bfs, names.arg=unique(elementMetadata(bfs)[,1]),col=rainbow(length(unique(elementMetadata(bfs)[,1])))))
Try(tkmessageBox(title="EDASeq Read Number",message="EDASeq read number plot is available in main R window",icon="info"))
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="arrow"))
}
################################################################################
"EDANtFreq" <- function(){
# require(EDASeq) || stop("Missing EDASeq library")
Try(whichArrayPlatform <- get("whichArrayPlatform",envir=affylmGUIenvironment))
if(whichArrayPlatform ==""){
Try(tkmessageBox(title="QC",message="No arrays have been loaded. Please try New or Open from the File menu.",type="ok",icon="error"))
Try(tkfocus(.affylmGUIglobals$ttMain))
Try(return())
}
if(affylmGUIenvironment$NormalizedAffyData.Available & affylmGUIenvironment$NGS.Available){
Try(NormalizedAffyData <- get("NormalizedAffyData", env=affylmGUIenvironment))
Try(targets <- get("Targets", env=affylmGUIenvironment))
} else {
Try(tkmessageBox(title="NGS data set",message="Normalized data are not available.", type="ok", icon="error"))
Try(return())
}
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="watch"))
Try(bfs <- BamFileList(targets$FileName))
Try(pd <- DataFrame("name"=targets$Name, "Target"= targets$Target, row.names=paste(targets$Name, targets$Target, sep=".")))
Try(elementMetadata(bfs) <- pd)
Try(plot.names <- paste(unique(elementMetadata(bfs)[,1]), seq(1, length(unique(elementMetadata(bfs)[,1]))), sep=" = ", collapse=", "))
##selecting the bam to be plotted for mapping I.E. selecting the chromosome for the mapping
Try(ttcolExtract<-tktoplevel(.affylmGUIglobals$ttMain))
Try(tkwm.deiconify(ttcolExtract))
Try(tkgrab.set(ttcolExtract))
Try(tkfocus(ttcolExtract))
Try(tkwm.title(ttcolExtract,"Selecting the BAM file to be plotted"))
Try(tkgrid(tklabel(ttcolExtract,text=" ")))
Try(plotNtBam <- "")
Try(Local.colExtract <- tclVar(init=plotNtBam))
Try(entry.colExtract <-tkentry(ttcolExtract,width="4",font=.affylmGUIglobals$affylmGUIfont2,textvariable=Local.colExtract,bg="white"))
Try(tkgrid(tklabel(ttcolExtract,text=paste("Please enter the number associated to the sample of of interest\n", plot.names),font=.affylmGUIglobals$affylmGUIfont2)))
Try(tkgrid(entry.colExtract))
onOK <- function()
{
Try(assign("plotNtBam", as.numeric(tclvalue(Local.colExtract)),affylmGUIenvironment))
Try(tkgrab.release(ttcolExtract));Try(tkdestroy(ttcolExtract));Try(tkfocus(.affylmGUIglobals$ttMain))
}
Try(OK.but <-tkbutton(ttcolExtract,text=" OK ",command=onOK,font=.affylmGUIglobals$affylmGUIfont2))
Try(tkgrid(tklabel(ttcolExtract,text=" ")))
Try(tkgrid(OK.but))
Try(tkgrid.configure(OK.but))
Try(tkgrid(tklabel(ttcolExtract,text=" ")))
Try(tkfocus(entry.colExtract))
Try(tkbind(entry.colExtract, "<Return>",onOK))
Try(tkbind(ttcolExtract, "<Destroy>", function(){Try(tkgrab.release(ttcolExtract));Try(tkfocus(.affylmGUIglobals$ttMain));return(0)}))
Try(tkwait.window(ttcolExtract))
Try(tkfocus(.affylmGUIglobals$ttMain))
Try(plotNtBam <- get("plotNtBam", affylmGUIenvironment))
Try(plotNtFrequency(bfs[[plotNtBam]], main=unique(elementMetadata(bfs)[plotNtBam,1])))
Try(tkmessageBox(title="EDASeq Nt frequency",message=paste("EDASeq Nt frequency plot for sample", unique(elementMetadata(bfs)[plotNtBam,1]),"is available in main R window",icon="info")))
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="arrow"))
}
################################################################################
"EDAboxplot" <- function(){
# Try(require(EDASeq) || stop("Missing EDASeq library"))
Try(whichArrayPlatform <- get("whichArrayPlatform",envir=affylmGUIenvironment))
if(whichArrayPlatform ==""){
Try(tkmessageBox(title="QC",message="No arrays have been loaded. Please try New or Open from the File menu.",type="ok",icon="error"))
Try(tkfocus(.affylmGUIglobals$ttMain))
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="arrow"))
Try(return())
}
if(affylmGUIenvironment$NormalizedAffyData.Available & affylmGUIenvironment$NGS.Available){
Try(NormalizedAffyData <- get("NormalizedAffyData", env=affylmGUIenvironment))
Try(Targets <- get("Targets", env=affylmGUIenvironment))
} else {
Try(tkmessageBox(title="NGS data set",message="Normalized data are not available.", type="ok", icon="error"))
Try(return())
}
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="watch"))
Try(bowtieDirAvailable <- get("whichArrayPlatform",envir=affylmGUIenvironment))
Try(bowtieDirLocation.Available <- get("bowtieDirLocation.Available",envir=affylmGUIenvironment))
if(bowtieDirLocation.Available){
Try(bowtieDirLocation <- get("bowtieDirLocation",envir=affylmGUIenvironment))
} else{
Try(tkmessageBox(title="Bowtie data",message="It seems that Bowtie dir is missing!\nPlease install Bowtie using the function in General Tools menu",icon="error"))
Try(return())
}
#adding gc content to eset
Try(whichGenome <- annotation(NormalizedAffyData))
if(whichGenome == ""){
Try(tkmessageBox(title="Genome selection",message="No genome is indicated in the annotation slot of ExpressionSet",type="ok", icon="error"))
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="arrow"))
Try(return())
} else if (whichGenome == "hs19"){
Try(annlibname <- system.file("bowtie/hg19_gene-level.scaffold.Rda",package="oneChannelGUI"))
Try(load(annlibname))
} else if (whichGenome == "mm9"){
Try(annlibname <- system.file("bowtie/mm9_gene-level.scaffold.Rda",package="oneChannelGUI"))
Try(load(annlibname))
} else if (whichGenome == "rn4"){
Try(annlibname <- system.file("bowtie/rn4_gene-level.scaffold.Rda",package="oneChannelGUI"))
Try(load(annlibname))
} else{
Try(tkmessageBox(title="Genome selection",message="In the annotation slot of ExpressionSet is present a genome not annotated in oneChannelGUI!\nContact the maintainer for Genome implementation",type="ok", icon="error"))
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="arrow"))
Try(return())
}
#detecting the chr under analysis
Try(chr <- strsplit(Targets$FileName[1], "_")) #getting the chr
Try(chr <- as.vector(unlist(chr)))
Try(chr <- chr[length(chr)])
Try(chr <- sub(".bam", "", chr)) #needed to extract the right subset of gene-level annotation from makeGeneScaffold generated GRanges list
Try(chr <- sub("chr0", "chr", chr))
#selecting the chromosome genomic reanges on which assigning BAM data
Try(chr.gr <- chr.gr[which(names(chr.gr) == chr)])
Try(genes.lenght <- width(ranges(chr.gr[[1]])))
Try(names(genes.lenght) <- elementMetadata(chr.gr[[1]])$names)
Try(gc.freq <- gc.freq[which(names(gc.freq) == chr)])
Try(gc.freq <- unlist(gc.freq))
Try(tmp.names <- names(gc.freq))
Try(tmp.names <- sapply(tmp.names,function(x,chr){tmp<-sub(chr,'',x);return(tmp)},chr=paste(chr,'.', sep="")))
Try(tmp.names <- as.character(tmp.names))
Try(names(gc.freq) <- tmp.names)
if(identical(names(genes.lenght), names(gc.freq))){
Try(feature <- data.frame(gc=gc.freq,length=genes.lenght))
}else{
Try(gc.freq <- gc.freq[order(names(gc.freq))])
Try(genes.lenght <- genes.lenght[order(names(genes.lenght))])
Try(feature <- data.frame(gc=gc.freq,length=genes.lenght))
}
Try(var.tmp.pd<-data.frame(names(feature)))
Try(names(var.tmp.pd)<-"labelDescription" )
Try(rownames(var.tmp.pd)<-names(feature))
Try(tmp1.pd<-new("AnnotatedDataFrame", data=feature, varMetadata=var.tmp.pd))
#making eset featureNames identical to names gc.freq and genes.length
.myFeature <- function(eset){
tmp.names <- featureNames(NormalizedAffyData)
tmp.names <- sapply(tmp.names, function(x){sub('\\-_','#',x)})
tmp.names <- as.character(tmp.names)
tmp.names <- sapply(tmp.names, function(x){sub('\\+_','#',x)})
tmp.names <- as.character(tmp.names)
tmp.names <- sapply(tmp.names, function(x){tmp <- strsplit(x, '#');return(tmp[[1]][2])})
tmp.names <- as.character(tmp.names)
return(tmp.names)
}
Try(counts <- NormalizedAffyData)
Try(featureNames(counts) <- .myFeature(NormalizedAffyData))
Try(tmp1.pd <- tmp1.pd[which(featureNames(tmp1.pd)%in%featureNames(counts)),])
Try(counts <- counts[which(featureNames(counts)%in%featureNames(tmp1.pd)),])
Try(counts <- counts[order(featureNames(counts)),])
Try(tmp1.pd <- tmp1.pd[order(featureNames(tmp1.pd)),])
Try(eseq <- newSeqExpressionSet(exprs(counts), phenoData=pData(counts), featureData=tmp1.pd))
Try(names(pData(eseq))[1] <- "conditions")
Try(tkmessageBox(title="EDASeq Boxplot",message="Sample boxplot is available in main R window",icon="info"))
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="arrow"))
Try(boxplot(eseq, ylab="log10 counts"))
}
################################################################################
"EDAbiasPlot" <- function(){
# Try(require(EDASeq) || stop("Missing EDASeq library"))
Try(whichArrayPlatform <- get("whichArrayPlatform",envir=affylmGUIenvironment))
if(whichArrayPlatform ==""){
Try(tkmessageBox(title="QC",message="No arrays have been loaded. Please try New or Open from the File menu.",type="ok",icon="error"))
Try(tkfocus(.affylmGUIglobals$ttMain))
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="arrow"))
Try(return())
}
if(affylmGUIenvironment$NormalizedAffyData.Available & affylmGUIenvironment$NGS.Available){
Try(NormalizedAffyData <- get("NormalizedAffyData", env=affylmGUIenvironment))
Try(Targets <- get("Targets", env=affylmGUIenvironment))
} else {
Try(tkmessageBox(title="NGS data set",message="Normalized data are not available.", type="ok", icon="error"))
Try(return())
}
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="watch"))
Try(bowtieDirAvailable <- get("whichArrayPlatform",envir=affylmGUIenvironment))
Try(bowtieDirLocation.Available <- get("bowtieDirLocation.Available",envir=affylmGUIenvironment))
if(bowtieDirLocation.Available){
Try(bowtieDirLocation <- get("bowtieDirLocation",envir=affylmGUIenvironment))
} else{
Try(tkmessageBox(title="Bowtie data",message="It seems that Bowtie dir is missing!\nPlease install Bowtie using the function in General Tools menu",icon="error"))
Try(return())
}
#adding gc content to eset
Try(whichGenome <- annotation(NormalizedAffyData))
if(whichGenome == ""){
Try(tkmessageBox(title="Genome selection",message="No genome is indicated in the annotation slot of ExpressionSet",type="ok", icon="error"))
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="arrow"))
Try(return())
} else if (whichGenome == "hs19"){
Try(annlibname <- system.file("bowtie/hg19_gene-level.scaffold.Rda",package="oneChannelGUI"))
Try(load(annlibname))
} else if (whichGenome == "mm9"){
Try(annlibname <- system.file("bowtie/mm9_gene-level.scaffold.Rda",package="oneChannelGUI"))
Try(load(annlibname))
} else if (whichGenome == "rn4"){
Try(annlibname <- system.file("bowtie/rn4_gene-level.scaffold.Rda",package="oneChannelGUI"))
Try(load(annlibname))
} else{
Try(tkmessageBox(title="Genome selection",message="In the annotation slot of ExpressionSet is present a genome not annotated in oneChannelGUI!\nContact the maintainer for Genome implementation",type="ok", icon="error"))
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="arrow"))
Try(return())
}
#detecting the chr under analysis
Try(chr <- strsplit(Targets$FileName[1], "_")) #getting the chr
Try(chr <- as.vector(unlist(chr)))
Try(chr <- chr[length(chr)])
Try(chr <- sub(".bam", "", chr)) #needed to extract the right subset of gene-level annotation from makeGeneScaffold generated GRanges list
Try(chr <- sub("chr0", "chr", chr))
#selecting the chromosome genomic reanges on which assigning BAM data
Try(chr.gr <- chr.gr[which(names(chr.gr) == chr)])
Try(genes.lenght <- width(ranges(chr.gr[[1]])))
Try(names(genes.lenght) <- elementMetadata(chr.gr[[1]])$names)
Try(gc.freq <- gc.freq[which(names(gc.freq) == chr)])
Try(gc.freq <- unlist(gc.freq))
Try(tmp.names <- names(gc.freq))
Try(tmp.names <- sapply(tmp.names,function(x,chr){tmp<-sub(chr,'',x);return(tmp)},chr=paste(chr,'.', sep="")))
Try(tmp.names <- as.character(tmp.names))
Try(names(gc.freq) <- tmp.names)
if(identical(names(genes.lenght), names(gc.freq))){
Try(feature <- data.frame(gc=gc.freq,length=genes.lenght))
}else{
Try(gc.freq <- gc.freq[order(names(gc.freq))])
Try(genes.lenght <- genes.lenght[order(names(genes.lenght))])
Try(feature <- data.frame(gc=gc.freq,length=genes.lenght))
}
Try(var.tmp.pd<-data.frame(names(feature)))
Try(names(var.tmp.pd)<-"labelDescription" )
Try(rownames(var.tmp.pd)<-names(feature))
Try(tmp1.pd<-new("AnnotatedDataFrame", data=feature, varMetadata=var.tmp.pd))
#making eset featureNames identical to names gc.freq and genes.length
.myFeature <- function(eset){
tmp.names <- featureNames(NormalizedAffyData)
tmp.names <- sapply(tmp.names, function(x){sub('\\-_','#',x)})
tmp.names <- as.character(tmp.names)
tmp.names <- sapply(tmp.names, function(x){sub('\\+_','#',x)})
tmp.names <- as.character(tmp.names)
tmp.names <- sapply(tmp.names, function(x){tmp <- strsplit(x, '#');return(tmp[[1]][2])})
tmp.names <- as.character(tmp.names)
return(tmp.names)
}
Try(counts <- NormalizedAffyData)
Try(featureNames(counts) <- .myFeature(NormalizedAffyData))
Try(tmp1.pd <- tmp1.pd[which(featureNames(tmp1.pd)%in%featureNames(counts)),])
Try(counts <- counts[which(featureNames(counts)%in%featureNames(tmp1.pd)),])
Try(counts <- counts[order(featureNames(counts)),])
Try(tmp1.pd <- tmp1.pd[order(featureNames(tmp1.pd)),])
Try(eseq <- newSeqExpressionSet(exprs(counts), phenoData=pData(counts), featureData=tmp1.pd))
Try(names(pData(eseq))[1] <- "conditions")
Try(tkmessageBox(title="EDASeq Bias Plot",message="Sample bias plot is available in main R window",icon="info"))
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="arrow"))
Try(par(mfrow=c(2,2)))
#low resolution plot
Try(biasPlot(eseq, "gc", log=T, ylim=c(0,5)))
Try(biasPlot(eseq, "length", log=T, ylim=c(0,5)))
#high resolution plot
Try(biasPlot(eseq, "gc", log=T))
Try(biasPlot(eseq, "length", log=T))
}
###########################################################################################################
"fastQC" <-function(){
Try(binDir <- get("binDir",envir=affylmGUIenvironment))
Try(system(paste(binDir,"/fastqc",sep="")))
}
###########################################################################################################
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