plot-methods: Plotting function for ExomeDepth objects

In ExomeDepth: Calls Copy Number Variants from Targeted Sequence Data

Plotting function for ExomeDepth objects

Description

Plot function for the ExomeDepth class

Usage

## S4 method for signature 'ExomeDepth,ANY'
plot(
  x,
  sequence,
  xlim,
  ylim = NULL,
  count.threshold = 10,
  ylab = "Observed by expected read ratio",
  xlab = "",
  type = "b",
  pch = "+",
  with.gene = FALSE,
  col = "red",
  ...
)

Arguments

x	ExomeDepth object
sequence	character, Name of the sequence/chromosome of the region to plot (for example "chr5" would be typical)
xlim	numeric of size 2, start and end position of the region to plot
ylim	numeric of size 2, range for the y-axis
count.threshold	numeric, minimum number of reads in the reference set to display a point in the plot
ylab	Defaults to ”
xlab	Defaults to ”
type	Defaults to 'b'
pch	Defaults to '+'
with.gene	Logical, defaults to FALSE, Should the gene information (obtained from the annotation data) be plotted under the read depth plot?
col	character, Colour for the line displaying the read depth ratio for each exon
...	Additional arguments to be passed to the base plot function

ExomeDepth documentation built on Nov. 3, 2022, 5:05 p.m.