chrplot: Chromosom plot of CNVs

Description Usage Arguments Value Author(s)

View source: R/chrplot.R

Description

Display a chromosome view of the CNVs across samples

Usage

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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 Oct. 20, 2017, 12:58 a.m.