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, ...)
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). |
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 grid.rect ) |
main |
character vector specifying plot title. |
... |
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
y
flag
extras
Wolfgang Huber <huber@ebi.ac.uk>