chipAlongChrom1: Visualize ChIP intensities along the chromosome

Description

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.

Usage

chipAlongChrom1(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,  coord=NULL, verbose = TRUE, ...)

Arguments

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.

coord

optional integer of length 2; can be used instead of xlim to specify the start and end coordinates of the genomic region to plot

verbose

logical; progress output to STDOUT.

...

further parameters passed on to plot.default, see details

Value

invisible matrix of probe intensities in the selected genomic regions

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:

"r": restricted drawing of position-connecting lines. adjacent probe connections will be connected by a line only if less or equal to argument maxInterDistance apart from each other; each probe position will be marked by an individual point anyway (whose shape is determined by the argument ipch).

"u"

similar as "r" but the lines and the points will be unconnected; reminiscent of plot.default's type "b".

Examples

Run this code

  # 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
  chipAlongChrom1(exampleX, chrom="9", xlim=c(34318000,34321000),
                 ylim=c(-2,4), probeAnno=exProbeAnno, gff=exGFF)