Custom CNVR distribution map and plot all high frequency CNVR at once

Custom CNVR distribution map and plot all high frequency CNVR at once

cnvr_plot(
  cnvr,
  assembly = "ARS",
  overlap_cnvr = NULL,
  label_prop = TRUE,
  left_prop_label = 3,
  legend_x = 127,
  legend_y = 30,
  clean_cnv = NULL,
  sample_size = NULL,
  common_cnv_threshold = 0.05,
  refgene = "ARS",
  gain_col = "red",
  loss_col = "green",
  mixed_col = "blue",
  overlap_col = "purple",
  chr_col = "black",
  folder = "cnvr_plot",
  gene_font_size = 2.2,
  width_1 = 22,
  height_1 = 14.5,
  col_gene = "gray"
)

Arguments

cnvr

standard cnvr file was generated by 'call_cnvr' function
assembly

UMD = "Bovine UMD 3.1", ARS = "BOvine ARS UCD 1.2", "hg38" = "Human hg38", "hg19" = "Human hg19", Sheep = "Oar_v4.0", Pig = "Sscrofa11.1", Chicken = "Chicken_galGal6", Horse = "EquCab3.0", Dog = "UMICH_Zoey_3.1"
overlap_cnvr

the common CNVRs list between two CNVR results, which use to mark underline to indicate the common CNVRs, should only contain Chr, Start and End three columns, the standard file was generated by 'compare_cnvr' function
label_prop

if 'TRUE', will display the proportion of CNVRs in each chromosome
left_prop_label

adjust the coordinates of the label to move to the left, default value is 3
legend_x

the x coordinate of legend, relative to the maximum length of Chromosome, unit is 'Mb'
legend_y

the y coordinate of legend
clean_cnv

standard input file was generated by 'cnv_clean' function
sample_size

integer, the total number of unique samples in the cnv result. combine with common_cnv_threshold to plot all CNVs which passed the threshold
common_cnv_threshold

two decimal places, combine with sample_size to plot all CNVs passed the common threshold
refgene

reference gene list, use for plot gene
gain_col

set color for type of gain CNVR
loss_col

set color for type of loss CNVR
mixed_col

set color for type of mixed CNVR
overlap_col

set color for Overlapped CNVRs
chr_col

set color of Chromosomes
folder

set name of folder to save results
gene_font_size

set the font size of gene in CNV annotation plot
width_1

number to set the width of final plot size, unit is 'cm'
height_1

number to set the height of final plot size, unit is 'cm'
col_gene

set the color of Gene, only work in Gene annotated at CNV plot

Value

A figure of CNVR distribution map and plot parameters. If given clean_cnv file, will plot all CNVRs which are passed common threshold.