plotSegmentationHeatmap {tilingArray}R Documentation

Plot a heatmap diagram for a region along a chromosome

Description

Plot a heatmap diagram for a region along a chromosome

Usage

plotSegmentationHeatmap(dat, xlim, ylab, rowNames, 
                        chr=1, strand="+", vpr, colors,                 
                        colHeatmap=colorRamp(brewer.pal(9, "YlGnBu")), 
                        showConfidenceIntervals=TRUE, main, ...)

Arguments

dat list containing data to be plotted (see Details section below for particulars).
xlim integer vector of length 2 with start and end coordinates (in bases) for plotting.
ylab character scalar specifying y-axis label.
rowNames character vector specifying a name for each row in the heatmap plot.
chr integer of length 1 indicating the chromosome to plot (defaults to 1).
strand character scalar which should be set to either + or - to indicate which strand of DNA to plot the intensity values from (defaults to "+").
vpr which viewport to plot the figure in. If this function is called directly by the user this argument should be left missing.
colors named character vector, optional. If missing, a default color scheme is used: c("+"="#00441b", "-"="#081d58", "duplicated"="grey", "cp"="#101010", "highlight"="red", "threshold"="grey"), where the first three elements refer to colors of data points and the last three to those of lines in the plot.
colHeatmap function describing color scheme for the heatmap plot (defaults to YlGnBu from RColorBrewer package).
showConfidenceIntervals logical scalar indicating whether confidence intervals for each change-point are to be plotted (only available once segmentation has occurred).
main character vector specifying plot title.
... additional arguments.

Details

This function is called by plotAlongChrom when the argument what is set to heatmap. Although this function can be called directly by the user, this is not recommended. The dat list contains the following items: items x: x-coordinates (in bases) along chromosome,

  1. y: intensity matrix of probes along chromosome,
  2. flag: indicates probe uniqueness in the genome. Possibilities are 3: multiple perfect matches, 2: has no PM but one or more near-matches, 1: has exactly one PM and some near-matches in the genome, 0: has exactly one PM and no near-matches.
  3. extras: (optional) matrix of additional values (such as test-statistics/p-values) to be plotted.

Author(s)

Wolfgang Huber <huber@ebi.ac.uk>

Examples






[Package tilingArray version 1.16.0 Index]