R/getClinicData_MultipleCases.R

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

#' get Clinical Data for Multiple Cases. User needs to select at least one case to run this function. Get clinical data for more one or multiple cases.
#' @usage 
#' getClinicData_MultipleCases(getSummaryGSEAExists)
#' 
#' @param getSummaryGSEAExists  if equal to 0, the clinical data is displayed in table. if the argument is equal to 1, the clinical data is used to summarise GSEA analysis results.
#' 
#' @export
#' @return dataframe with clinical data
#' 
#' @examples 
#' ##Load Session
#' readRDS(paste(path.package("canceR"),"/extdata/rdata/brca_tcga73genes.rds", sep=""))
#' ## Select Case
#' ENV <- new.env(parent = emptyenv())
#' ENV$curselectCases <- 2
#' ## get Clinical data
#' \dontrun{
#' getClinicData_MultipleCases(getSummaryGSEAExists = 0)
#' }
#' 
getClinicData_MultipleCases <- function(getSummaryGSEAExists){
    
    ##getSummaryGSEAExists is an argument for the function getSummaryGSEA(). this function accept only one clinical dats.
    if(is.null(ENV$curselectCases) || length(ENV$curselectCases) ==0){
        msgNoCases <- "Select at less one Case"
        tkmessageBox(message=msgNoCases)
        stop(msgNoCases) 
        
    }else if(getSummaryGSEAExists == 1 && 
             length(ENV$curselectCases) > 1){

            tkmessageBox(message=paste("Multiple Cases are loaded. To get Summary of GSEA Results, 
                                   Select only the Clinical data of study on which are you working."),icon="warning")
            stop("Multiple Cases are loaded. To get Summary of GSEA Results, 
             Select only the Clinical data of study on which are you working.")
            
            print(paste("length(ENV$curselectCases): ", length(ENV$curselectCases)))

        }else if(getSummaryGSEAExists == 0 &&
                 length(ENV$curselectCases) != 0){
            
            ClinicalData <- 0
            
            for(c in seq(ENV$curselectCases)){
                Study_id <- ENV$CasesRefStudies[ENV$curselectCases[c]]
                print(ENV$curselectCases[c])
                print(ENV$CasesRefStudies)
                print(paste0("Study_id: ", Study_id))
                
                #study_id <- gsub('_[a-z]*[0-9]*$', '', Study_id)
                ## extract only abbreviation of studies
                # unique(
                #     grep(paste(
                #         unique(unlist(lapply(selected_by_curser, 
                #                              function(x) unlist(strsplit(x,split = "_"))[1]))),
                #         collapse = "|"), checked_Studies, value=TRUE)
                # )
                
                ClinicalData <- cBioPortalData::clinicalData(ENV$cgds, Study_id) |>
                    select("sampleId", everything()) 
                #data.frame(row.names = 1)

                if(nrow(ClinicalData)==0){
                    msgNoClinData=paste("No Clinical Data are Available for\n", ENV$CasesStudies[ENV$curselectCases[c]+2])
                    tkmessageBox(message=msgNoClinData, title= paste("Study: ", ENV$StudyRefCase[c]))
                } else{
                    
                    ttClin<-tktoplevel()
                    tktitle(ttClin) <- paste0("Clinical Data of"," ",ENV$CasesStudies[ENV$curselectCases[c]+2])
                    tkwm.geometry(ttClin, "430x420")
                    yscr1 <- tkscrollbar(ttClin, repeatinterval=2,
                                         command=function(...)tkyview(ttc,...))
                    xscr1 <- tkscrollbar(ttClin, repeatinterval=2,orient="horizontal",
                                         command=function(...)tkxview(ttc,...))
                    ttc<-tklistbox(ttClin,height=20, width= 50 ,selectmode="multiple",
                                   xscrollcommand=function(...)tkset(xscr1,...),
                                   yscrollcommand=function(...)tkset(yscr1,...),background="white")
                    
                    tkgrid(ttc,yscr1, columnspan=1)
                    tkgrid.configure(yscr1,rowspan=20, columnspan=1,sticky="nsw")
                    tkgrid(xscr1,columnspan=2)
                    tkgrid.configure(xscr1,rowspan=2,columnspan=2,sticky="ew")
                    
                    tkinsert(ttc,"end","All")
                    cbIValue=0
                    for(j in 1: ncol(ClinicalData)){
                        tkinsert(ttc,"end",names(ClinicalData)[j])
                    }
                    
                    OnOK <- function(){
                        ENV$curselect <- as.numeric(tkcurselection(ttc))+1
                        
                        if(ENV$curselect[1]=="1"){
                            ENV$ClinicalData <- ClinicalData
                            
                            title <- paste0(ENV$StudyRefCase[c],": ", ENV$CasesStudies[ENV$curselectCases[c]+2])
                            getInTable(ENV$ClinicalData, title)
                            tkdestroy(ttClin)
                        } else{
                            #ENV$ClinicalData <- ClinicalData[!(is.na(ClinicalData[,ENV$curselect]) | ClinicalData[,ENV$curselect]==""), ] 
                            ENV$ClinicalData <- ClinicalData[ENV$curselect-1]
                            
                            title=paste(ENV$StudyRefCase[c],
                                        ENV$CasesStudies[ENV$curselectCases[c]+1], sep=": ")
                            getInTable(ENV$ClinicalData, title)
                            
                            tkdestroy(ttClin)
                        }
                    }
                    OK.but <- tkbutton(ttClin,text="OK",command=OnOK)
                    tkgrid(OK.but,columnspan=2)
                    
                    ##Waiting to checkbox before to access to the next clinical data
                    tkwait.window(ttClin)
                }

                ##getSummaryGSEA funtion needs return(ClinicalSub_All)
                if(getSummaryGSEAExists==1){
                    return(ENV$ClinicalData)
                }
            }
        }
    
    
}