R/getMutData.R

In canceR: A Graphical User Interface for accessing and modeling the Cancer Genomics Data of MSKCC

#' get Mutation data for multiple genes
#' @usage
#' getMutData()
#'
#' @return a a dataframe with mutation informations
#' @export
#'
#' @examples
#' readRDS(paste(path.package("canceR"),"/extdata/rdata/ucec_tcga_pubGSEA1021.rds", sep=""))
#' \dontrun{
#' getMutData()
#' }
#' 
getMutData <- function(){
    
    tclRequire("BWidget")
    tclRequire("Tktable")
   
        testCheckedCaseGenProf()
       
        Lchecked_Studies <- myGlobalEnv$curselectCases
        Lchecked_Cases <- length(myGlobalEnv$curselectCases_forStudy)
        Lchecked_GenProf <- length(myGlobalEnv$curselectGenProfs_forStudy)
        
        MutData=0
        MutData_All <-NULL
        MutDataSub<-0
        MutDataSub_All <- NULL
        
        for(c in 1:length(myGlobalEnv$curselectCases)){
            
            GenProf<-myGlobalEnv$GenProfsRefStudies[myGlobalEnv$curselectGenProfs[c]]
            if (length(grep("mutation", GenProf))==0){
                msgNoMut <- "Select Mutation data from Genetics Profiles"
                tkmessageBox(message = msgNoMut, icon='info')
                break
            }
            Case<- myGlobalEnv$CasesRefStudies[myGlobalEnv$curselectCases[c]]
         
            MutData <- getMutationData(myGlobalEnv$cgds,Case, GenProf, myGlobalEnv$GeneList)
            
            if(length(MutData[,1])==0){
                msgNoMutData=paste("No Mutation Data are Available for\n", myGlobalEnv$CasesStudies[myGlobalEnv$curselectCases[c]+1])
                tkmessageBox(message=msgNoMutData, title= paste(myGlobalEnv$StudyRefCase[c],myGlobalEnv$CasesStudies[myGlobalEnv$curselectCases[c]+1], myGlobalEnv$GenProfsStudies[myGlobalEnv$curselectGenProfs[c]+1], sep=": "))
                
                
            } else{
                ttMutData_cb <- tktoplevel()
                tktitle(ttMutData_cb) <- paste(myGlobalEnv$StudyRefCase[c],myGlobalEnv$CasesStudies[myGlobalEnv$curselectCases[c]+1], myGlobalEnv$GenProfsStudies[myGlobalEnv$curselectGenProfs[c]+1], sep=": ")
                            
                cbAll <- tkcheckbutton(ttMutData_cb)
                cbAllValue <- tclVar("0")
                tkconfigure(cbAll,variable=cbAllValue)
                labelAll<- tklabel(ttMutData_cb,text= "All")
                tkgrid(labelAll, cbAll)
                
                cbIValue=0
                for(i in 1: length(names(MutData))){
                    
                    cbi <- paste ("cb", i, sep="")  
                    cbi <- tkcheckbutton(ttMutData_cb)
                    cbiValue <- paste("cb", i, "Value", sep="")
                    cbIValue[i] <- cbiValue
                    cbIValue[i] <- tclVar("0")
                    
                    tkconfigure(cbi,variable=cbiValue)
                    labeli <- paste ("label", i , sep="") 
                    labelI <- labeli
                    labelI <- tklabel(ttMutData_cb,text= names(MutData[i]))
                    tkgrid(labelI,cbi)
                }
                
                OnOK <- function(){
                    
                    cbAllVal <- as.character(tclvalue(cbAllValue))
                    if(cbAllVal =="1"){
                        
                        title=paste(myGlobalEnv$StudyRefCase[c],myGlobalEnv$CasesStudies[myGlobalEnv$curselectCases[c]+1], myGlobalEnv$GenProfsStudies[myGlobalEnv$curselectGenProfs[c]+1], sep=": ")
                        getInTable(MutData, title=title)
                       
                    } else{
                        
                        
                        for (i in 1: length(names(MutData))){
                            cbiValue <- paste("cb", i, "Value", sep="")
                            cbIValue <- cbiValue
                            cbiVal <- paste("cb", i, "Val", sep="")
                            cbIVal<-cbiVal
                            
                            cbIVal[i] <- as.character(tclvalue(cbIValue))
                            if (cbIVal[i]=="1"){
                                
                                ## convert metacharacter "[""]" not supported by tclarray()
                                #MutData_All[i]<- gsub("\\[Not Available\\]","NA", MutData[i])
                                MutDataSub <- cbind(MutDataSub, MutData[i])
                                
                            }
                            
                        }
                        MutDataSub<-MutDataSub[-1]
                        #MutDataSub_All[[c]]<<- MutDataSub
                        Sys.chmod(getwd(), mode = "0777", use_umask = TRUE)
                        #MutDataSub_All[[c]]<<- as.data.frame.array(MutDataSub, envir=.GlobalEnv)
                        #myGlobalEnv$MutDataSub_All[[c]] <- as.list.data.frame(MutDataSub, envir=myGlobalEnv)
                        
                        
                        name <- paste("MutDataSub", c, sep="")
                        #Sys.chmod(getwd(), mode = "0777", use_umask = TRUE)
                        assign(name, MutDataSub, envir=myGlobalEnv)
                        
                        title=paste(myGlobalEnv$StudyRefCase[c],myGlobalEnv$CasesStudies[myGlobalEnv$curselectCases[c]+1], myGlobalEnv$GenProfsStudies[myGlobalEnv$curselectGenProfs[c]+1], sep=": ")
                        getInTable(MutDataSub, title=title)
                      
                    }
                    
                    tkdestroy(ttMutData_cb)
                }         
                
                OK.but <- tkbutton(ttMutData_cb,text="OK",command=OnOK)
                tkgrid(OK.but)
                
                ##Waiting to checkbox before to access to the next clinical data
                tkwait.window(ttMutData_cb)
            }
            
        }
   }