cnv_summary_plot: Summary plots for CNVs

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

Description

Make summary graphs for CNVs. Types of plots produced include: * CNV counts by length and copy number * Length distribution by copy number * CNV counts by chromosome and copy number * CNV counts by individual

Usage

cnv_summary_plot(
  clean_cnv,
  length_group = c(0.05, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 1, 2, 5),
  plot_sum_1 = FALSE,
  plot_sum_2 = FALSE,
  folder = "cnv_summary_plot",
  col_0 = "hotpink",
  col_1 = "turquoise",
  col_2 = "gray",
  col_3 = "tomato",
  col_4 = "deepskyblue",
  height_sum1 = 26,
  width_sum1 = 20,
  height_sum2 = 20,
  width_sum2 = 27
)

Arguments

clean_cnv	a clean CNV file, as generated by the 'clean_cnv' function
length_group	a vector of lengths (in Mb) to classify CNV lengths for plotting. For example, the vector ‘c(0.05, 0.3, 0.6, 1)', instructs the function to divide the CNV lengths into four groups: ’<0.05Mb', '0.05 - 0.3Mb', '0.3-0.6Mb' and '>1Mb'. Up to 11 values can be provided.
plot_sum_1	plot the first type of summary plot combination
plot_sum_2	plot the second type of summary plot combination
folder	set the name of the output folder
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
height_sum1	height of Summary Plot 1 (in cm)
width_sum1	width of Summary Plot 1 (in cm)
height_sum2	height of Summary Plot 2 (in cm)
width_sum2	width of Summary Plot 2 (in cm)

Value

Some summary pictures

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