R/plot_cnvr_source.R

In JH-Zhou/HandyCNV: HandyCNV: An R package for Standardized Summary, Annotation, Comparison, and Visualization of CNV, CNVR and ROH

#' Plotting CNVs by the source information
#'
#' @param cnvr standard file was generated by 'call_cnvr' function, should contain the frequency of CNVR
#' @param clean_cnv standard file was generated by 'cnv_clean' function
#' @param pedigree include 'Sample_ID', 'Father_ID', 'Mother_ID', 'Country', 'Group'
#' @param Frequent_threshold Integer, indicate the frequency of CNVR
#' @param height_1 set the height of plot
#' @param width_1 set the width of plot
#' @param col_0 set color for 0 copy of CNV
#' @param col_1 set color for 1 copy of CNV
#' @param col_2 set color for 2 copy of CNV (which might be ROH)
#' @param col_3 set color for 3 copy of CNV
#' @param col_4 set color for 4 copy of CNV
#' @param report_id report the sample ID while plotting
#' @param folder set the folder to save results
#'
#' @return CNVR source plot
#' @export plot_cnvr_source
#'
plot_cnvr_source <- function(cnvr, clean_cnv, pedigree, Frequent_threshold, height_1 = 30, width_1 = 15, col_0 = "hotpink",  col_1 = "turquoise", col_2 = "gray", col_3 = "tomato", col_4= "deepskyblue", report_id = TRUE, folder = "plot_cnvr_source") {
  cnvr <- fread(cnvr)
  high_freq <- filter(cnvr, n_Sample >= Frequent_threshold)
  print(paste0(nrow(high_freq), " CNVRs passed Frequent_threhold..."))

  for (i in 1:nrow(high_freq)){
    cnv_visual(clean_cnv = clean_cnv,
               chr_id = high_freq$Chr[i],
               start_position = high_freq$Start[i]/1000000,
               end_position = high_freq$End[i]/1000000,
               report_id = report_id,
               pedigree = pedigree,
               height_1 = height_1,
               width_1 = width_1,
               col_0 = col_0,  col_1 = col_1, col_2 = col_2, col_3 = col_3, col_4= col_4,
               folder = folder)
    print(paste0("Plotting the ", i, " th CNVRs"))
  }
}