plotSegmentationDots {tilingArray} | R Documentation |
Plot points for a region along a chromosome
plotSegmentationDots(dat, xlim, ylim, ylab, threshold=NA, chr=1, strand="+", vpr, colors, main, pointSize=unit(0.6, "mm"), showConfidenceIntervals=TRUE, sepPlots=FALSE, cexAxisLabel=1, cexAxis=1,...)
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. |
ylim |
numeric vector containing the y limits of the plot. |
ylab |
character scalar (if sepPlots=FALSE ) or vector containing y-axis label(s). |
threshold |
numeric scalar indicating the threshold of expression (default value is NA, for
no threshold. If a value is supplied, it is subtracted from the intensity measures in dat$y . |
chr |
integer of length 1 indicating the chromosome to be plot (defaults to 1). |
strand |
character scalar which should be set to either + or - to
indicate which strand of DNA to plot the intensity values from (defaults to "+"). |
vpr |
which viewport to plot the figure in. If this function is called directly by the user this argument should be left missing. |
colors |
named character vector, optional. If missing,
a default color scheme is used:
c("+"="#00441b", "-"="#081d58", "duplicated"="grey", "cp"="#101010",
"highlight"="red", "threshold"="grey") ,
where the first three elements refer to the colors of data points and the
last three to the colors of lines in the plot. |
main |
character vector specifying plot title. |
pointSize |
an object of class unit which specifies the size of each point. Default value is unit(0.6, "mm") . |
showConfidenceIntervals |
logical scalar indicating whether confidence intervals for each change-point are to be plotted (only available once segmentation has occurred). |
sepPlots |
logical scalar indicating whether the intensities are plotted separately for each array (if dat$y has multiple columns). Defaults to FALSE, in which case the average intensity for each probe is plotted. When TRUE, up to 3 arrays can be plotted separately (more than 3 gets crowded). |
cexAxisLabel |
numeric scalar specifying the magnification to be used for the y-axis label relative to the current test size. |
cexAxis |
numeric scalar specifying the magnification to be used for the y-axis annotation relative to the current text size. |
... |
additional arguments. |
This function is called by plotAlongChrom
when the argument what
is set to dots
. 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,
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>