plot_segments: Plot segmented files.

In sean-cho/Epicopy: Get CNV information from 450K array

Description

Plots segmentation output for individual samples.

Usage

plot_segments(CNA, which_sample, threshold = 0.15, ylab = "Copy Number",
  xlab = "Genomic Location (kb)", ylim = c(-2, 2), title = NULL,
  seg_lwd = 2, seg_col = c("skyblue3", "black"), ...)

Arguments

CNA	CNA output from LRRtoCNA
which_sample	Either a numeric/integer to indicate which sample to plot or a character vector with the sample name.
threshold	Numeric vector indicating where to plot dotted lines to indicate threshold. Defaults at 0.15.
ylab	Y-axis labels
xlab	X-axis labels
ylim	Y-axis limits
title	Title. Defaults to sample name with Epicopy segmentation string.
seg_lwd	Line width of the segments
...	Passes arguments to plot to control everything other than segment.

Details

epicopy Plot resulting segments from LRRtoCNA.

Plots the segmentation results from LRRtoCNA.

Value

Segment plots.

See Also

getLRR LRRtoCNA export_gistic RGChannelSet-class read.450k.sheet read.450k.exp

Examples

# Load included example data.
data(data_vignette)
# Plot
plot_segments(epi_seg, which_sample = 1)

sean-cho/Epicopy documentation built on May 29, 2019, 4:24 p.m.