chrplot: Chromosom plot of CNVs

In jmonlong/PopSV: Population-based detection of structural variants from Read-Depth signal

Description

Display a chromosome view of the CNVs across samples

Usage

chrplot(cnv.df, type = c("sample", "stacked"), bin.size = 5e+05,
  chr.df = NULL, showSampleNames = FALSE, chr.prefix = FALSE,
  chr.position = c("vertical", "packed"), show.all.chr = FALSE)

Arguments

cnv.df	a data.frame with the CNVs (columns 'chr', 'start', 'end') for each sample (column 'sample')
type	the type of graph to display. 'stacked' (default) shows the frequency line-graph across the chromosome. 'sample' shows a heatmap with each row representing one sample.
bin.size	the bin size. Default is 1e6.
chr.df	a data.frame with the chromosome boundaries.
showSampleNames	should the sample names be displayed. Default is FALSE (it quickly becomes unreadable).
chr.prefix	Is there a 'chr' prefix in the chromosome names. Default is FALSE
chr.position	How should the chromosome be arranged. Default is 'vertical', other option is 'packed'.
show.all.chr	Should all the chromosomes be displayed (even if no CNVs) ? Default is FALSE, i.e. only chr with CNVs are displayed.

Value

a ggplot graph object

Author(s)

Jean Monlong

jmonlong/PopSV documentation built on Sept. 15, 2019, 9:29 p.m.