R/plot_cbs_segs.R

In PoisonAlien/maftools: Summarize, Analyze and Visualize MAF Files

#' Plots segmented copy number data.
#' @details this function takes segmented copy number data and plots it. If MAF object is specified, all mutations are highlighted on the plot.
#' @param cbsFile CBS segmented copy number file. Column names should be Sample, Chromosome, Start, End, Num_Probes and Segment_Mean (log2 scale).
#' @param maf optional \code{\link{MAF}}
#' @param tsb If segmentation file contains many samples (as in gistic input), specify sample name here.
#' Defualt plots head 1 sample. Set 'ALL' for plotting all samples. If you are maping maf, make sure sample names in
#' Sample column of segmentation file matches to those Tumor_Sample_Barcodes in MAF.
#' @param savePlot If true plot is saved as pdf.
#' @param ylims Default NULL
#' @param seg_size Default 0.1
#' @param width width of plot
#' @param height height of plot
#' @param genes If given and maf object is specified, maps all mutataions from maf onto segments. Default NULL
#' @param ref.build Reference build for chromosome sizes. Can be hg18, hg19 or hg38. Default hg19.
#' @param writeTable If true and if maf object is specified, writes plot data with each variant and its corresponding copynumber to an output file.
#' @param removeXY don not plot sex chromosomes.
#' @param color Manually specify color scheme for chromosomes. Default NULL. i.e, aletrnating Gray70 and midnightblue
#' @return Draws plot
#' @export
#' @examples
#' tcga.ab.009.seg <- system.file("extdata", "TCGA.AB.3009.hg19.seg.txt", package = "maftools")
#' plotCBSsegments(cbsFile = tcga.ab.009.seg)
#'

plotCBSsegments = function(cbsFile = NULL, maf = NULL, tsb = NULL, savePlot = FALSE, ylims = NULL, seg_size = 0.1,
                           width = 6, height = 3, genes = NULL, ref.build = 'hg19', writeTable = FALSE, removeXY = FALSE, color = NULL){

  if(is.null(cbsFile)){
    stop('Missing segmentation file!')
  }

  #Read segmentation file and change chromosome names
  seg = readSegs(seg = cbsFile)

  if(removeXY){
    seg = seg[!Chromosome %in% c('23', '24')]
  }

  seg = seg[order(as.numeric(Chromosome))]
  data.table::setkey(x = seg, Chromosome, Start_Position, End_Position)

  #If user doesn't provide sample name
  if (is.null(tsb)){
    #Use top 1 sample for simplicity
    tsb = unique(as.character(seg[,Sample]))[1]
    message("No 'tsb' specified, plot head 1 sample. Set tsb='ALL' to plot all samples.")
  } else if (tsb == "ALL") {
    #Number of unique samples in segmentation file
    tsb = unique(as.character(seg[,Sample]))
  }

  for(i in 1:length(tsb)){

    if(savePlot){
      pdf(file = paste(tsb[i], '_segPlot.pdf', sep = ''), width = width, height = height, bg = "white", paper = "special")
    }

    plotCBS(segData = seg, tsb = tsb[i], build = ref.build, chr.colors = color,
            y_lims = ylims, rect_size = seg_size)

    if(!is.null(maf)){
      tsb.mapped = mapMutsToSegs(seg = seg, maf = maf, tsb = tsb[i], build = ref.build)
      if(writeTable){
        write.table(x = tsb.mapped[,.(Hugo_Symbol, Chromosome, Start_Position, End_Position, Tumor_Sample_Barcode, Segment_Start, Segment_End, Segment_Mean, CN)],
                    file = paste(tsb[i], '_segData.tsv', sep = ''), sep='\t', quote = FALSE, row.names = FALSE)
      }
    }

    if(!is.null(genes)){
      if(is.null(maf)){
        warning("Missing maf file. Skipping gene mapping..", immediate. = TRUE)
      }else{
        #Map mutations to segments
        tsb.mapped.cn = tsb.mapped[Hugo_Symbol %in% genes]

        if(nrow(tsb.mapped.cn) > 0){
          text(x = tsb.mapped.cn$Start_Position_updated,
               y = ifelse(test = tsb.mapped.cn$Segment_Mean > 0, yes = tsb.mapped.cn$Segment_Mean+1, no = tsb.mapped.cn$Segment_Mean - 1),
               labels = as.character(tsb.mapped.cn$Hugo_Symbol), cex = 0.8)
          segments(x0 = tsb.mapped.cn$Start_Position_updated, y0 = tsb.mapped.cn$Segment_Mean,
                   x1 = tsb.mapped.cn$Start_Position_updated,
                   y1 = ifelse(test = tsb.mapped.cn$Segment_Mean > 0, yes = tsb.mapped.cn$Segment_Mean+0.9, no = tsb.mapped.cn$Segment_Mean - 0.9),
                   lty = 1)
        }else{
          message(paste0("No mutations observed from given gene list for sample ", tsb[i]))
        }
      }
    }
    if(savePlot){
      dev.off()
    }
  }
 return(invisible(NULL))
}