R/Gedit.R

In libcell/deconvBench: A tool for approaches evaluation of cell fraction estimation

#' Gedit
#'#' Title
#' @param bulkdata  A matrix with genes in rows and samples in columns.
#' @param signature A data-frame containing signatures of different cell types.
#' @importFrom reticulate source_python
#' @importFrom utils  write.table
#' @return A data frame of Mixed cellular fractions.
#' @export
#'
#' @examples
#' # Bulk <- Bulk_GSE60424
#' # res <- Gedit(bulkdata = Bulk,
#' #              signature = LM22)

Gedit <- function(signature, bulkdata) {

   wd_a <- getwd()

  bulkdata <- bulkdata[apply(bulkdata, 1, var)!=0,]

  Gedit_tmp_path <- tempdir()

  Gedit_filepath <- paste0(Gedit_tmp_path,"/result_Gedit/")


  if(file.exists(Gedit_filepath)){
    path <- Gedit_filepath
  }else{
    dir.create(Gedit_filepath)
  }

  Symbol <- rownames(bulkdata)
  bulkdata <- cbind(Symbol,bulkdata)
  write.table(bulkdata, paste0(Gedit_filepath,"Bulkdata.tsv"),
              sep ="\t", row.names = F,col.names = T)

  symbol <- rownames(signature)
  signature <- cbind(symbol,signature)
  signature <- rbind(colnames(signature),signature)
  write.table(signature, paste0(Gedit_filepath,"Signature.tsv"),sep = "\t",
              col.names = F,row.names = F)


  probpath <- system.file(package = "deconvBench")

  GEDIT_probpath <- paste0(probpath,"/python/rpytools/GEDIT/")

  setwd(GEDIT_probpath)

  code <-  paste0("python3 ", GEDIT_probpath,"GEDIT2.py",
                  " -mix ",Gedit_filepath,"Bulkdata.tsv",
                  " -ref ",Gedit_filepath,"Signature.tsv",
                  " -outFile ",Gedit_filepath,"res_Gedit.tsv")
  system(code)

  res_Gedit <- read.table(paste0(Gedit_filepath,"res_Gedit.tsv"),sep = "\t",row.names = 1,header = T)

  setwd(wd_a)

  return(res_Gedit)

}