R/Draw_MLnet.R

In YUZIXD/scMLnet: The Construction of Multi-layer Singaling Network

#' @title Save and Draw the Multi-layer Signaling Network
#'
#' @param MLnetList The output of Run_MLnet function.
#' @param LigClu character: The neighboring cell
#' @param RecClu character: The central cell
#' @param outdir The name of output folder
#' @param PyHome The path to PYTHONHOME. The PyHome parameter is invalidated if only the plotMLnet parameter is set to TRUE.
#' @param plotMLnet Whether to draw the multi-layer signaling network. The default setting is FALSE.
#'
#' @description
#' This  function save the results generated by Rub_scMLnet function and visualize the results by pymnet package (python).
#' The generated multi-layer signaling network is saved in the folder named by the LigClu, RecClu and outdir parameters.
#'
#' @export
#'
#' @return NULL
DrawMLnet <- function(MLnetList,LigClu,RecClu,outdir = NULL,PyHome,plotMLnet = F){

  #creat output workdir
  if(!file.exists("output")){ dir.create("output") }
  i <- paste(strsplit(LigClu,split = "\\W")[[1]][1],strsplit(RecClu,split = "\\W")[[1]][1],sep = "_")
  if(is.null(outdir)){
    wd <- paste("./output",i,sep = "/")
    if(!file.exists(wd)){dir.create(wd)}
  }else{
    wd <- paste("./output",outdir,sep = "/")
    if(!file.exists(wd)){dir.create(wd)}
    wd <- paste("./output",outdir,i,sep = "/")
    if(!file.exists(wd)){dir.create(wd)}
  }

  #output
  LigRecNet <- MLnetList[[1]]
  RecTFNet <- MLnetList[[2]]
  TFTarNet <- MLnetList[[3]]

  #output result
  cat("Save Results\n")
  NetLigRecFile <- paste(wd,"LigRec.net.txt",sep = "/")
  NetRecTFFile <- paste(wd,"RecTF.net.txt",sep = "/")
  NetTFTarFile <- paste(wd,"TFTarGene.net.txt",sep = "/")
  writeLines(LigRecNet,con=NetLigRecFile,sep="\n")
  writeLines(RecTFNet,con=NetRecTFFile,sep="\n")
  writeLines(TFTarNet,con=NetTFTarFile,sep="\n")

  #draw MLnet
  if(plotMLnet){

    cat("Draw MLnet!\n")

    #check python home
    if(is.null(PyHome)){stop("Can't find python!")}

    #figure path
    netPic <- paste(wd,"mulnet.pdf",sep = "/")

    #draw
    cmd <- paste(PyHome,"./code/DrawNetNew.py",NetLigRecFile,NetRecTFFile,NetTFTarFile,netPic,sep=" ")
    system(cmd)

  }

  cat("Finish!\n")

}