plot_cnvr_panorama: Plotting CNVR with all relevant information

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

Description

Plotting CNVR with all relevant information

Usage

plot_cnvr_panorama(
  cnvr,
  cnv_annotation,
  intensity = NULL,
  map = NULL,
  prefix_bed = NULL,
  ld_heat = TRUE,
  sample_size,
  common_cnv_threshold = 0.05,
  width_1 = 14,
  height_1 = 30,
  folder = "cnvr_panorama",
  col_0 = "hotpink",
  col_1 = "turquoise",
  col_2 = "NA",
  col_3 = "tomato",
  col_4 = "deepskyblue",
  col_gene = "black",
  gene_font_size = 2.2
)

Arguments

cnvr	cnvr list, standard file generated by the call_cnvr function
cnv_annotation	standard file generated by the call_gene function
intensity	the signal intensity file contains LRR and BAF
map	the map corresponding to the reference genome used to create the CNVR file, standard file generated by the convert_map function
prefix_bed	the prefix of the BED, BIM and FAM files in Plink format
ld_heat	If TRUE, will plot a heatmap of LD, otherwise will plot the classic inverted triangle plot. Plotting is faster with TRUE, and plotting the triange with FALSE may fail for large regions.
sample_size	the total number of unique samples in the CNVR list
common_cnv_threshold	two decimal places, combine with sample_size to set the common threshold
width_1	default value is 14, unit is 'cm', set the width of final the plot
height_1	default value is 30, unit is 'cm', set the height of final the plot
folder	set the folder name to save results in
col_0	set colour for 0 copy of CNV
col_1	set colour for 1 copy of CNV
col_2	set colour for 2 copy of CNV (which might be ROH)
col_3	set colour for 3 copy of CNV
col_4	set colour for 4 copy of CNV
col_gene	set colour of genes
gene_font_size	set the font size of gene labels in CNV annotated plot

Value

cnvr plot with all CNVs, annotated genes, Log R Ratio, B Allele Frequency, Genotyping rate and LD...

JH-Zhou/HandyCNV documentation built on Dec. 18, 2021, 12:25 a.m.