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,
  highlight = NULL,
  assembly = "hg38"
)

Arguments

data	The frequency object returned by pgxLoader function.
chrom	A vector with chromosomes to be plotted. If NULL, return the plot by 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 to indicate which filter to be plotted, such as 1 (the first filters in data slot of object ) or 'NCIT:C4038' (specific filter name). The length of filters is limited to one if the parameter circos is False. Default is 1.
circos	A logical value to indicate if return a circos plot. If TRUE, it can return a circos plot with multiple filters for display and comparison. Default is FALSE.
highlight	Indices of genomic bins to be highlighted with red color.
assembly	A string specifying which genome assembly version should be applied to CNV frequency plotting. Allowed options are "hg19", "hg38". Default is "hg38" (genome version used in Progenetix).

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="frequency", output ='pgxfreq', filters="NCIT:C3512")
## visualize
pgxFreqplot(freq)

progenetix/pgxRpi documentation built on May 7, 2024, 2:57 p.m.