chipAlongChrom {Ringo} | R Documentation |
This function can visualize the array intensities from a ChIP chip
experiment for a chromosomal region or the whole chromosome. It's
loosely based on the plotAlongChrom
function from the package
tilingArray
, but provides a different visualization.
chipAlongChrom(eSet, chrom, probeAnno, xlim, ylim = NULL, samples = NULL, paletteName = "Dark2", colPal = NULL, byStrand = FALSE, ylabel = "fold change [log]", rugCol = "#000010", itype = "r", ipch = 20, icex = 1, ilwd = 3, ilty = 1, useGFF = TRUE, gff = NULL, featCol = "darkblue", zero.line = TRUE, putLegend = TRUE, add = FALSE, maxInterDistance = 200, verbose = TRUE, ...)
eSet |
An expression set containing the (normalized) ChIP
intensities. Can be generated by using the function
asExprSet . |
chrom |
character; the chromosome to visualize |
probeAnno |
Environment holding genomic position, index and gene
association of probes on array. See scripts/makeProbeAnno.R
for how to generate such an environment. |
xlim |
start and end genomic coordinates on the chromosome to visualize |
ylim |
minimum and maximum probe intensities for the plot, if
NULL (default) set as range(exprs(eSet)) |
samples |
numeric; which samples from the eSet are to be
shown. Default is to show all samples in the eSet , |
paletteName |
character; Name of the RColorBrewer palette to use for sample colors. If the number of samples is greater than the palette size, random colors are taken. |
colPal |
vector of colors to use for the sample intensities.
This is alternative to the argument paletteName
for specifying which colors to use. |
byStrand |
logical; not implemented yet. |
ylabel |
character; label for the y-axis, passed on to the
plotting function as ylab |
rugCol |
color to use for marking the probe positions on the x-axis (genomic coordinate) |
itype |
character; type of plot type to use for the sample
intensities. Can be "r","u", or any of the type
specifications used in plot.default .
Defaults to "r". Please refer to the details section below. |
ipch |
plot character to use with itype="p" |
icex |
character expansion to use for plotting symbol |
ilwd |
line width of plotted lines if itype="l" |
ilty |
line type of plotted lines if itype="l" ; passed on
to par(lty) . |
useGFF |
use further annotation |
gff |
Data frame containing annotation for genomic feature to be used to further annotate the plot. |
featCol |
color to use for genomic features. |
zero.line |
logical; should a dashed horizontal line at y=0 be put into the plot? |
putLegend |
logical; should a legend be put into the plot? |
add |
logical; should expression set intensities be plotted onto current device instead of a new one? |
maxInterDistance |
numeric; only used when itype is either
"r" or "u"; specifies the maximal distance up to which
adjacent probe positions should be connected by a line. |
verbose |
logical; progress output to STDOUT. |
... |
further parameters passed on to plot.default , see
details |
The following plot.default
arguments are already defined by
arguments of this function and thus may not be included in ...
:
xlim, ylim, col, pch, cex, lwd, lty, frame.plot
The itype
argument specifies the desired type of plot. It can
be any valid specification of the type
argument in
plot.default
or one of two special types:
maxInterDistance
apart
from each other; each probe position will be marked by an
individual point anyway (whose shape is determined by the argument
ipch
).plot.default
's
type
"b".
invisible
matrix of probe intensities in the selected
genomic regions
Use the function alongChrom
for
alternative ways to display probe intensities in genomic regions.
Joern Toedling toedling@ebi.ac.uk
plot.default
;
plotAlongChrom
in package tilingArray
# load data ringoExampleDir <- system.file("exData",package="Ringo") load(file.path(ringoExampleDir,"exampleProbeAnno.rda")) load(file.path(ringoExampleDir,"exampleX.rda")) # show a gene that is well represented on this microarray chipAlongChrom(exampleX, chrom="9", xlim=c(34318000,34321000), ylim=c(-2,4), probeAnno=exProbeAnno, gff=exGFF)