plot_segmentation: Plot segmentation profile

In mskcc/facets-suite: Functions to run and parse output from FACETS

Plot segmentation profile

Description

Creates an IGV-like graphical representation of the copy-number segments across the samples in a segmentation object, as output by run_facets.

Usage

plot_segmentation(segs, plotX = FALSE, sample_order = NULL,
  cap_log_ratios = TRUE, colors = c("darkblue", "white", "red"),
  return_object = FALSE)

Arguments

segs	FACETS segment output, IGV formatted.
plotX	If TRUE, includes chromosome X.
sample_order	Manual order of samples.
cap_log_ratios	Cap log-ratios at the absolute value.
colors	Vector of three colors, giving the low-, mid- and high-point of the color scale.
return_object	If TRUE, returns ggplot2 object instead of printing plot.

Value

Output plots in viewer, unless return_object is used and ggplot2 objects are returned.

mskcc/facets-suite documentation built on Sept. 13, 2022, 4:14 a.m.