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 = "Intensity", rugCol = "#000010", itype = "p", ipch ="-", icex = 3, ilwd = 2, ilty = 1, useGFF = TRUE, gff = NULL, featCol = "darkblue", zero.line = TRUE, putLegend = TRUE, add = FALSE, verbose = TRUE, ...)
eSet |
An expression set containing the (normalized) ChIP
intensitites. Can be generated by using the function
asExprSet . |
chrom |
character; the chromosome to visualizate |
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 (defaul) set as range(exprs(eSet)) |
samples |
numerc; 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 above the paletter 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. Defaults to "p". |
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? |
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
returns 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
ringoExampleDir <- system.file("exData",package="Ringo") load(file.path(ringoExampleDir,"exampleProbeAnno.rda")) load(file.path(ringoExampleDir,"exampleX.rda")) chipAlongChrom(exampleX, chrom="8", xlim=c(60208500,60216000), ylim=c(-1,6), colPal=2:3, probeAnno=exProbeAnno, gff=exGFF)