R/wrapperClustersIntegration.R

In kendomaniac/rCASC: rCASC reproducible Classification Analysis of Single Cell Sequencing Data

#' @title integrationCircos
#' @description This function execute toprnk analysis which search for correspondence between clusters of two different experiments requires that the data are clustered with any of the software implemented in rCASC, cometsc, bulkClusters and autoencoder4pseudoBulk were already executed.   
#' @param group, a character string. Two options: sudo or docker, depending to which group the user belongs
#' @param scratch.folder, a character string indicating the path of the scratch folder
#' @param file.matrix1, a character string indicating the path of the first matrix 
#' @param file.matrix2, a character string indicating the path of the second matrix 
#' @param separator1, separator used in count file, e.g. '\\t', ','
#' @param separator2, separator used in count file, e.g. '\\t', ','
#' @param cl1, path of clustering.output for file.matrix1
#' @param cl2, path of clustering.output for file.matrix2
#' @param permutation, number of permutation to be run
#' @param seed, integer file necessary for reproducibility
#' @param top.ranked, MAX number of top comet genes to be used for each cluster, default 320
#' @param file.total1, a character string indicating the path to the total.csv.for the 1st dataset to be integrated. Total.csv is generated with autoencoder4pseudoBulk. File, with file name and extension included. 
#' @param file.total2, a character string indicating the path to the total.csv.for the 2nd dataset to be integrated. Total.csv is generated with autoencoder4pseudoBulk. File, with file name and extension included. 
#' @param gsea, default msigdb.all, which includes all classes. List of the available GSEA classes: c1.all, c2.cgp, c2.cp.biocarta, c2.cp.kegg, c2.cp.pid, c2.cp.reactome, c2.cp.wikipathways, c3.all, c3.mir, c3.tft.gtrd, c3.tft, c4.cgn, c4.cm, c5.go.bp, c5.go.cc, c5.go.mf, c5.hpo, c6.all, c7.all, c8.all, h.all, msigdb.all. Please note that msigdb.all includes all gsea classes.
#' @param X, X parameter for the XLmHG, default 5, for more info please see XLmHG help: https://xl-mhg.readthedocs.io/en/latest/.
#' @param L, L parameter for the XLmHG, default 0.15, for more info please see XLmHG help: https://xl-mhg.readthedocs.io/en/latest/.
#' @param pvalue, XLmHG pvalue threshold,default 0.05
#' @param outputFolder, where results are placed
#' @author Luca Alessandri, alessandri [dot] luca1991 [at] gmail [dot] com, University of Torino
#'
#' @return A picture called integrated_score.png and a file called integrated_score.csv and all the final_scores.csv used to produce the integrated results. 
#' @examples
#' \dontrun{
#'  library(rCASC)
#'  wrapperClustersIntegration(group="docker", 
#'         scratch.folder="/scratch", 
#'         file.matrix1="/data/clusters_association_paper/setA1_set1/setA1/VandE/VandE.csv",
#'         file.matrix2="/data/clusters_association_paper/setA1_set1/set1/VandE/VandE.csv",
#'         cl1="/data/clusters_association_paper/setA1_set1/setA1/VandE/Results/VandE/5/VandE_clustering.output.csv",
#'         cl2="/data/clusters_association_paper/setA1_set1/set1/VandE/Results/VandE/4/VandE_clustering.output.csv",
#'         file.total1="/data/clusters_association_paper/setA1_set1/setA1/VandE/Results/setA1/permutation/total.csv",
#'         file.total2="/data/clusters_association_paper/setA1_set1/set1/VandE/Results/set1/permutation/total.csv",
#'         separator1=",", separator2=",", 
#'         permutation=100, seed=111, top.ranked=320, gsea="msigdb.all", X=5, L=0.15, pvalue=0.05,
#'         outputFolder="/data/clusters_association_paper/setA1_set1"
#'         )
#'}
#' @export
wrapperClustersIntegration <- function(group=c("sudo","docker"), scratch.folder, 
                                       file.matrix1, file.matrix2, 
                                       file.total1, file.total2, 
                                       cl1, cl2, 
                                       separator1, separator2, 
                                       permutation=100, seed=111,
                                       top.ranked=320, 
                                       gsea="msigdb.all", X=5, L=0.15, pvalue=0.05,
                                       outputFolder){
  #NOTE some controls needs to be added to check that everything is in place
  cat("\nRunning gseaXLmHG\n")
  comet.folder1 <- sub(basename(cl1), "", cl1)
  comet.folder1 <- paste(comet.folder1, "outputdata", sep="/")
  comet.folder2 <- sub(basename(cl2), "", cl2)
  comet.folder2 <- paste(comet.folder2, "outputdata", sep="/")
  gseaXLmHG <- function(group=group, scratch.folder=scratch.folder, xCometFolder=comet.folder1, yCometFolder=comet.folder1, 
                        gsea=gsea, X=X, L=L, pvalue=pvalue, separatorX=separator1, separatorY=separator1, outputFolder=outputFolder)
  
  cat("\nRunning seuratIntegrationPermutation\n")
  seuratIntegrationPermutation(group=group, scratch.folder=scratch.folder, 
                               file1=file.matrix1, file2=file.matrix2, separator1=separator1, 
                               separator2=separator1, cl1=cl1, cl2=cl2, permutation=permutation, 
                               seed=seed, outputFolder=paste(outputFolder, "ISC", sep="/"))
  
  cat("\nRunning toprnk\n")
  file.pblk1.tmp <- paste(sapply(strsplit(basename(file.matrix1), "\\."), function(x)x[1]), "_bulkRow", sep="")
  file.pblk1.tmp1 <- sapply(strsplit(basename(file.matrix1), "\\."), function(x)x[2])
  file.pblk1 <- sub(basename(file.matrix1), "", file.matrix1)
  file.pblk1 <- paste(file.pblk1,file.pblk1.tmp,".",file.pblk1.tmp1, sep="")
  
  file.pblk2.tmp <- paste(sapply(strsplit(basename(file.matrix2), "\\."), function(x)x[1]), "_bulkRow", sep="")
  file.pblk2.tmp1 <- sapply(strsplit(basename(file.matrix2), "\\."), function(x)x[2])
  file.pblk2 <- sub(basename(file.matrix2), "", file.matrix2)
  file.pblk2 <- paste(file.pblk2,file.pblk2.tmp,".",file.pblk2.tmp1, sep="")
  
  toprnk(group=group, scratch.folder=scratch.folder, fileX=file.pblk1, fileY=file.pblk2, 
         separatorX=separator1, separatorY=separator2, xCometFolder=comet.folder1, yCometFolder=comet.folder2, 
         top.ranked=top.ranked, outputFolder=outputFolder)
  
  cat("\nRunning integrationPblkae\n")
  integrationPblkae(group=group, scratch.folder=scratch.folder, fileX=file.total1, fileY=file.total2, outputFolder=outputFolder)
  
  cat("\nRunning integrationCircos\n")
  gsea.file=paste(outputFolder, "GSEA/final_score.csv", sep="/")
  isc.file=paste(outputFolder, "ISC/final_score.csv", sep="/")
  XYpb.file=paste(outputFolder, "/XYpb/XYpb_final_score.csv", sep="/")
  pblkae.file=paste(outputFolder, "pblkae/final_score.csv", sep="/")
  
  integrationCircos(group=group, scratch.folder=scratch.folder, gsea.file=gsea.file, isc.file=isc.file, XYpb.file=XYpb.file, pblkae.file=pblkae.file, outputFolder=outputFolder)
  
}