chipAlongChrom1 {Ringo} | R Documentation

## 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

### 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".

### Value

`invisible` matrix of probe intensities in the selected genomic regions

### Note

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

### Author(s)

Joern Toedling

### See Also

`plot.default`; `plotAlongChrom` in package `tilingArray`

### Examples

      # 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)

[Package Ringo version 1.51.0 Index]