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# Project: BiclustGUI
#
# Author: Gebruiker
###############################################################################
#which: all, range (from..to..), selection (vector)
#dim (row, col, both)
# DO SOME CHECKS HERE:
# 1: is there an active dataset?
# 2: is the dimension of the active dataset corresponding with the biclust result ?
ExtractBiclustersGUI <-function(result,which="all",from=1,to=1,selection=c(1),dim="both",save=FALSE,save.name="Extract"){
# Which biclusters to select?
if(which=="all"){
selected_biclusters <- seq(1,result@Number,1)
}
if(which=="range"){
selected_biclusters <- seq(from,to,1)
}
if(which=="selection"){
selected_biclusters <- selection
}
# eval(parse(text=paste0("matrixdata <- as.matrix(",ActiveDataSet(),")")))
matrixdata <- as.matrix(get(ActiveDataSet(),envir=.GlobalEnv))
# Making the desired list object
out <- list()
names_temp <- c()
for(i.bc in 1:length(selected_biclusters)){
i.bc.sel <- selected_biclusters[i.bc]
names_temp <- c(names_temp,paste0("bicluster_",i.bc.sel))
out_temp <- list()
if(dim=="row"|dim=="both"){
out_temp$rows <- which(result@RowxNumber[,i.bc.sel]==TRUE)
out_temp$rows.names <- rownames(matrixdata)[out_temp$rows]
}
if(dim=="col"|dim=="both"){
out_temp$cols <- which(result@NumberxCol[i.bc.sel,]==TRUE)
out_temp$cols.names <- colnames(matrixdata)[out_temp$cols]
}
out[[i.bc]] <- out_temp
}
names(out) <- names_temp
if(save==TRUE){
eval(parse(text=paste0(save.name," <- out")))
path.temp <- getwd()
path.temp <- paste0(path.temp,"/",save.name,".RData")
eval(parse(text=paste0("save(",save.name,",file='",path.temp,"')")))
temp.command <- paste0("warning('The result is saved in ",path.temp,"',call.=FALSE)")
justDoIt(temp.command)
}
return(out)
}
ExtractBiclustersGUI_general <- function(result,which="all",from=1,to=1,selection=c(1),dim="both",save=FALSE,save.name="Extract"){
temp <- .tobiclust(result)
return(ExtractBiclustersGUI(temp,which=which,from=from,to=to,selection=selection,dim=dim,save=FALSE,save.name="Extract"))
}
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