R/browse2.R

In IsoGeneGUI: A graphical user interface to conduct a dose-response analysis of microarray data

`browse2` <-
function() {

    file <- tclvalue(tkgetOpenFile(filetypes=
        gettext('{"R Data Files" {".rda" ".Rdata" ".RDA"}} {"All Files" {"*"}}')))
    assign("file",file,envir=.GlobalEnv)
    
if (file == "")
 { 
  tkmessageBox(message = "No file was selected!")
return()
}
else {
      SAMResdata <- load(file)
    #assign("SAMResdata",SAMResdata ,envir=.GlobalEnv)
      
chPval <-tktoplevel()
tkwm.title(chPval ,"Obtaining previous SAM permutation ") 
tkgrab.set(chPval )
tkfocus(chPval )
      spec.frm <- tkframe(chPval ,borderwidth=2)
frame1 <- tkframe(spec.frm, relief="groove", borderwidth=2)
buttonFrameiso <-tkframe(chPval ,borderwidth=2)

      scr <- tkscrollbar( spec.frm , repeatinterval=2, command=function(...)tkyview(tl,...))

      tl <-tklistbox(spec.frm,height=5,selectmode="single",yscrollcommand=function(...)tkset(scr,...),background="white")

for (i in (1:length(SAMResdata)))
{
    tkinsert(tl,"end",SAMResdata[i])
}
tkselection.set(tl,0)

lab0 <- tklabel(chPval ,text="Choose the object contain the raw p-values")
lab1 <- tklabel(spec.frm,text="  ")
tkgrid(lab0)

tkgrid(lab1,lab1,tl,scr)
tkgrid.configure(tl,sticky="nse")
tkgrid.configure(scr,rowspan=10,sticky="nsw")
tkgrid(frame1)


    ######
    onCancel <- function()
  {
    ReturnVal <- 0
      tkgrab.release(chPval )
tkdestroy(chPval )
tkwm.deiconify(chPval) 
       tkfocus(chPval)
 }
   OnOK <- function()
{
     SAMResChoice <- SAMResdata [as.numeric(tkcurselection(tl))+1]
tclvalue(pvalName) <<- file 

SAMRes <- get(SAMResChoice)
    assign("SAMRes.temp",SAMRes ,envir=.GlobalEnv)

 try(SAMResID <- rownames(SAMRes$aa1))
      exprsID <- rownames(exprs)
      matchID <- match (SAMResID ,exprsID )
      exprs2SAM <- exprs[matchID ,]
DirectionSAM <- SAMRes [[11]][matchID ]
    assign("matchID.temp",matchID ,envir=.GlobalEnv)
    assign("exprs2SAM.temp",exprs2SAM  ,envir=.GlobalEnv)
 assign("DirectionSAM",DirectionSAM,envir=.GlobalEnv)

N <- length(matchID)
 MeanDiffSAM  <<- MeanDiff (dose,exprs2SAM )

   tkdelete(treeWidget,"nodeSAM")  
 try( tkdelete(treeWidget,"PermSAMNode"), silent=T)
      tkinsert(treeWidget,"end","Record4Node","PermSAMNode",text="SAM Permutations ")
tkinsert(treeWidget,"end","PermSAMNode","NumGeneSAMNode",text= paste("Number genes analyzed: ",N )  )
tkinsert(treeWidget,"end","PermSAMNode","FudgeNode",text= paste("Fudge Factor: ",SAMRes [[13]] ) )
tkinsert(treeWidget,"end","PermSAMNode","NumpermSAMNode",text= paste("Number permutations: ",SAMRes [[12]])  )
   tkdestroy(chPval)
      }

  
   OK.but <-tkbutton(buttonFrameiso ,text="   OK   ",command=OnOK)
   Cancel.but <-tkbutton(buttonFrameiso ,text=" Cancel ",command=onCancel)
   tkgrid(OK.but,Cancel.but)

   tkgrid(spec.frm)
   tkgrid(buttonFrameiso)
   tkfocus(chPval)
   }
   
}