pgxFreqplot: Plot CNV frequency data

In progenetix/pgxRpi: R wrapper for Progenetix

Plot CNV frequency data

Description

Thie function plots the frequency of deletions and duplications

Usage

pgxFreqplot(
  data,
  chrom = NULL,
  layout = c(1, 1),
  filters = NULL,
  circos = FALSE,
  assembly = "hg38"
)

Arguments

data	CNV frequency object returned by the pgxLoader or segtoFreq functions.
chrom	A vector specifying which chromosomes to plot. If NULL, the plot will cover the entire genome. If specified, the frequencies are plotted with one panel for each chromosome. Default is NULL.
layout	Number of columns and rows in plot. Only used in plot by chromosome. Default is c(1,1).
filters	Index or string value indicating which filter to plot. The length of filters is limited to one if the parameter circos is FALSE. Default is the first filter.
circos	A logical value indicating whether to return a circos plot. If TRUE, it returns a circos plot that can display and compare multiple filters. Default is FALSE.
assembly	A string specifying the genome assembly version to apply to CNV frequency plotting. Allowed options are "hg19" and "hg38". Default is "hg38".

Value

The binned CNV frequency plot

Examples

## load necessary data (this step can be skipped in real implementation)
data("hg38_cytoband")
## get frequency data
freq <- pgxLoader(type="cnv_frequency", output ='pgxfreq', filters="NCIT:C3512")
## visualize
pgxFreqplot(freq)

progenetix/pgxRpi documentation built on Nov. 4, 2024, 11:31 p.m.