R/demo.default.R

In Durenlab/scREG: RegNMF

#demo.default <- function(in_foldername,out_foldername,fragment,macs2path,bedtoolspath,chr,from,to,core,width=6,height=4){
demo.default <- function(in_foldername,out_foldername,fragment,macs2path,awkpath,core){


  element=read_ATAC_GEX.default(in_foldername)
  W123H=RegNMF.default(E=element$E,
                 O=element$O,
                 Symbol=element$Symbol,
                 PeakName=element$PeakName,
                 Symbol_location=element$Symbol_location,
                 Peak_location=element$Peak_location)

  ans=clustering.default(W123H$H)
  groupName=SplitGroup.default(foldername=out_foldername,
                     barcord=element$barcode[,1],
                     W3=W123H$W3,
                     H=W123H$H,
                     Reg_symbol_name=W123H$Reg_gene_name,
                     Reg_peak_name=W123H$Reg_peak_name,
                     cluster=ans$S[1,])

  visual_need=callpeak.default(outfolder=out_foldername,
                               fragment=fragment,
                               barcord_cluster_whole=groupName["barcordFileName"],
                               oldRegFolder=groupName["RegFolderName"],
                               macs2path=macs2path,
                               awkpath=awkpath,
                               cluster=unique(ans$S[1,]),
                               clusterL=length(ans$S[1,]))

#  clusterlist=unique(ans$S[1,])

#  Visualization.default(wholef=in_foldername,
#                        peakf=visual_need["peak_clusterF"],
#                        regf=visual_need["RE_clusterF"],
#                        chr=chr,
#                        from=from,
##                        to=to,
#                        clusterlist=clusterlist,
#                        width=width,height=height)


  return(ans);

}