plot-ReadCounts: Diagnostic Plots for Read Counts

In ChIPseqR: Identifying Protein Binding Sites in High-Throughput Sequencing Data

Description

Produces plots to assess the distribution of reads, either for an entire chromosome or within a (small) window.

Usage

## S4 method for signature 'ReadCounts,missing'
plot(x, chr, center, score, width=2000, type=c("hilbert", "window"), ...)
## S4 method for signature 'RLEReadCounts,missing'
plot(x, chr, center, score, width=2000, type=c("hilbert", "window"), ...)

Arguments

x	Object of class ReadCounts or RLEReadCounts.
chr	Index or name of chromosome for which read counts should be plotted.
center	For type ‘window’, the center coordinate of the window to plot.
score	For type ‘window’, an object of type BindScore (or BindScore) that should be used to include information about the score and predicted binding sites into the plot.
width	For type ‘window’, the width of the window.
type	Character string indicating the type of plot that should be produced (see details).
...	Further arguments (see details).

Details

Type ‘window’ produces a plot that shows read counts as vertical bars. If score is not missing, it is used to plot the score and predicted binding sites (if any) as well. Any additional arguments are passed on to .plotWindow.

Type ‘hilbert’ produces a Hilbert curve plot of read counts for an entire chromosome. Additional arguments are passed on to .plotReads.

Value

Called for its side effect.

Author(s)

Peter Humburg

See Also

hilbertImage

ChIPseqR documentation built on Nov. 8, 2020, 6:49 p.m.