plot_variants: Plot variants in genes or regions

In fridoling/isomutR: isomutR

Description

plot_variants plots the variants of an isomut file within a set of genes or regions.

Usage

plot_variants(
  isomut,
  regions,
  annotation = gtf_scer,
  ymax = NULL,
  fill = NULL,
  bar_width = NULL,
  flank = 50,
  showGenes = TRUE,
  fontsize = NULL,
  dy = NULL,
  filename = NULL,
  ...
)

Arguments

isomut	a data.frame or data.table of isomut data as generated by read_isomut.
regions	either a character vector of gene names or a GRanges object.
annotation	path to annotation file in gtf or gff format or GRanges object containing the annotations.
ymax	maximum of variants to plot.
fill	isomut column to use for fill color (default is mut_freq).
bar_width	width of the bars (default 5).
flank	additional space left and right of genes (in bp).
showGenes	whether to show genes in the plot (only works with annotation).
fontsize	font size for gene and chromosome names.
dy	width of gene/chromosome bars.
filename	optionally specify file name.
...	additional parameters for ggsave (e.g. width and height).

fridoling/isomutR documentation built on Jan. 21, 2022, 4:45 a.m.