plot_frequencies: plot genome-wide amplification and deletion frequencies

In SingerLab/gac: Genetic Analysis of Cells

plot genome-wide amplification and deletion frequencies

Description

plot genome-wide amplification and deletion frequencies

Usage

plot_frequencies(
  cnr,
  genes = FALSE,
  cols = c("#D40000", "#318CE7"),
  xlab = "Genome",
  ylab = "Alteration Frequency",
  ylim = c(-1, 1),
  ...
)

Arguments

cnr	a cnr bundle
genes	logical, if TRUE use AmpFQ from gene data instead of bin, Default FALSE
cols	colors for amplifications and deletions, default to red and blue
xlab	x-axis label, passed to plot
ylab	y-axis label, passed to plot
ylim	sets coordinate space for y-axis, defaults to -1 to 1. The text will show absolute values for the deletion frequenies
...	other arguments to plot

Value

Returns a bin alteration frequency plot with amplifications on the top axis, and deletions on the bottom axis.

Examples

data(cnr)
cnr <- get_alteration_frequencies(cnr)

plot_frequencies(cnr)
plot_frequencies(cnr, xaxs = "i", bty = "n")

SingerLab/gac documentation built on March 29, 2025, 4:38 p.m.