chipAlongChromOld: Visualize ChIP intensities along the chromosome
In Ringo: R Investigation of ChIP-chip Oligoarrays

Description Usage Arguments Details Value Note Author(s) See Also Examples

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.

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, ...)

`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

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".

invisible matrix of probe intensities in the selected genomic regions

Use the function alongChrom from package geneplotter fo an alternative way to display probe intensities in genomic regions.

Joern Toedling

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