genoPlot-methods: Plot data along the genome

In genoset: A RangedSummarizedExperiment with methods for copy number analysis

Description

Plot location data and chromosome boundaries from a GenoSet or GRanges object against data from a numeric or Rle. Specifying a chromosome name and optionally a 'xlim' will zoom into one chromosome region. If more than one chromosome is present, the chromosome boundaries will be marked. Alternatively, for a numeric x and a numeric or Rle y, data in y can be plotted at genome positions x. In this case, chromosome boundaries can be taken from the argument locs. If data for y-axis comes from a Rle lines are plotted representing segments. X-axis tickmarks will be labeled with genome positions in the most appropriate units.

Usage

genoPlot(x, y, ...)

## S4 method for signature 'numeric,numeric'
genoPlot(x, y, add = FALSE, xlab = "",
  ylab = "", col = "black", locs = NULL, ...)

## S4 method for signature 'numeric,Rle'
genoPlot(x, y, add = FALSE, xlab = "",
  ylab = "", col = "red", locs = NULL, lwd = 2, xlim = NULL, ...)

## S4 method for signature 'GenoSetOrGenomicRanges,ANY'
genoPlot(x, y, chr = NULL,
  add = FALSE, pch = ".", xlab = "", ylab = "", ...)

Arguments

x	GenoSet (or descendant) or GRanges
y	numeric or Rle
...	Additional plotting args
add	Add plot to existing plot
xlab	character, label for x-axis of plot
ylab	character, label for y-axis of plot
col	character, color to plot lines or points
locs	GRanges, like rowRanges slot of GenoSet
lwd	numeric, line width for segment plots from an Rle
xlim	integer, length two, bounds for genome positions. Used in conjunction with 'chr' to subset data for plotting.
chr	Chromosome to plot, NULL by default for full genome
pch	character or numeric, printing character, see points

Value

TRUE

Methods

signature(x = 'GenoSetOrGenomicRanges', y = 'ANY')

Plot feature locations and data from one sample.

signature(x = 'numeric', y = 'numeric')

Plot numeric location and a vector of numeric data.

signature(x = 'numeric', y = 'Rle')

Plot numeric location and a vector of Rle data. Uses lines for Rle runs.

See Also

Other 'genome plots': genomeAxis

Examples

data(genoset,package='genoset')
genoPlot( x=genoset.ds,y=genoset.ds[,1,'lrr'] )
genoPlot( genoPos(genoset.ds), genoset.ds[,1,'lrr'], locs=rowRanges(genoset.ds) ) # The same
genoPlot( 1:10, Rle(c(rep(0,5),rep(3,4),rep(1,1))) )

genoset documentation built on Nov. 8, 2020, 6:07 p.m.