[BioC] Question (vennDiagram vs. topTable) + Patch (plotTitle for vennDiagram) for AffylmGUI 1.3.0

[Steffen Moeller]

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")
   {