Dear list, dear James and dear Ken, the selection for a particular P value in the topTable of affylmGUI and the selection of genes differentially expressed in the vennDiagram of affylmGUI show different numbers. This is most likely of no surprise since the probabilities might have different semantics. Does anybody have a hint for me how to get the topTable output in sync with the vennDiagram? Or should I instead construct the vennCounts from the results of the topTable function? Is anybody working on extending affylmGUI for an analysis of associated GO terms? Kind regards and many thanks for affylmGUI Steffen The patch below adds a title to the vennDiagram, distinguishing between the title for the tk Window (plotTitleOuter) and the one to be saved as part of the diagram (plotTitleInner). --- affylmgui-1.3.0.orig/R/plot.R +++ affylmgui-1.3.0/R/plot.R @@ -893,18 +893,11 @@ Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="arrow")) - plotVennDiagram <- function() - { - Try(opar<-par(bg="white")) - Try(vennDiagramaffylmGUI(vc,include=include,names=as.vector(setNames), cex=0.85,mar=rep(1,4))) - Try(TempGraphPar<-par(opar)) - } - Try(LocalHScale <- .affylmGUIglobals$Myhscale*1.25) Try(LocalVScale <- .affylmGUIglobals$Myvscale*1.25) # FIXME: It'd be nice to list the one, two or three parameters. - Try(plotTitle <- paste("Venn diagram for contrast parameterization",ContrastParameterizationNamesVec[contrastPa rameterizationIndex])) + Try(plotTitleOuter <- paste("Venn diagram for contrast parameterization",ContrastParameterizationNamesVec[contr astParameterizationIndex])) Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="watch")) Try(p.value <- 0.01) @@ -929,10 +922,27 @@ Try(if (length(setNames)==0) return()) + Try(plotTitleInner<-paste("Contrasts of ",limmaDataSetNameText," at P-Value ",p.value,sep="")) + Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="arrow")) + Try(tkfocus(.affylmGUIglobals$ttMain)) + Try(plotTitleList <- GetPlotTitle(plotTitleInner)) + Try(if (length(plotTitleList)==0) return()) + Try(plotTitleInner <- plotTitleList$plotTitle) + + plotVennDiagram <- function() + { + Try(opar<-par(bg="white")) + Try(vennDiagramaffylmGUI(vc,include=include,names=as.vector(setNames), + main=plotTitleInner,cex=0.85,mar=rep(1,4) + ) + ) + Try(TempGraphPar<-par(opar)) + } + Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="watch")) Try(tkfocus(.affylmGUIglobals$ttMain)) Try(ttVennDiagramPlot <- tktoplevel(.affylmGUIglobals$ttMain)) - Try(tkwm.title(ttVennDiagramPlot,plotTitle)) + Try(tkwm.title(ttVennDiagramPlot,plotTitleOuter)) Try(if (.affylmGUIglobals$graphicsDevice=="tkrplot") {