plotSegmentationHeatmap {tilingArray} | R Documentation |
Plot a heatmap diagram for a region along a chromosome
plotSegmentationHeatmap(dat, xlim, ylab, rowNames, chr=1, strand="+", vpr, colors, colHeatmap=colorRamp(brewer.pal(9, "YlGnBu")), showConfidenceIntervals=TRUE, just=c("left","centre"), main,makeRasterImage = TRUE, ...)
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 |
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:
|
colHeatmap |
function describing color scheme for the heatmap plot (defaults to
|
showConfidenceIntervals |
logical scalar indicating whether confidence intervals for each change-point are to be plotted (only available once segmentation has occurred). |
just |
character vector specifying the justification of the
supplied values to the given coordinates; setting the first entry to
"left" indicates that the supplied x-coordinates are the start
positions of the probes, change this to "centre" if the
x-coordinates are the probe middle positions. Usually the second
entry should be "centre" (see |
main |
character vector specifying plot title. |
makeRasterImage |
logical scalar indicating whether to plot the heatmap image
by the grid.raster (see |
... |
additional arguments. |
This function is called by plotAlongChrom
if 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:
x
x-coordinates (in bases) along chromosome
y
intensity matrix of probes along chromosome
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.
extras
(optional) matrix of additional values (such as test-statistics/p-values) to be plotted
Wolfgang Huber <huber@ebi.ac.uk>
data(segnf) data(gffSub) nmLabel = colnames(segnf$"1.+"@y) plotAlongChrom(segnf,chr=1,coord=c(35000,50000),what="heatmap", gff=gffSub,rowNamesHeatmap=nmLabel) ##using raster image