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ExomeDepth (version 1.1.16)

plot-methods: Plotting function for ExomeDepth objects

Description

Plot function for the ExomeDepth class

Usage

# S4 method for 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