chipAlongChrom {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 based on the `plotAlongChrom` function from the package `tilingArray`, but provides a different visualization.

### Usage

    ## S4 method for signature 'ExpressionSet,probeAnno'
    plot(x, y, ...)

    chipAlongChrom(eSet,  probeAnno, chrom, xlim, ylim,
     samples = NULL, paletteName = "Set2", colPal = NULL,
     ylab = "Fold change [log]", ipch = 16, ilwd = 3, ilty = 1,
     icex = 3, gff = NULL,
     featureExclude=c("chromosome", "nucleotide_match","insertion"),
     zeroLine = TRUE, sampleLegend = TRUE, sampleLegendPos = "topleft",
     featureLegend = FALSE, maxInterDistance = 200,  coord = NULL,
     highlight, main, ...)

### Arguments

`eSet` | An expression set containing the (normalized) ChIP intensities, e.g. the result objects from functions `preprocess` and `computeRunningMedians`.
`x` | Corresponds to argument `eSet` when calling the S4 method
`probeAnno` | An object of class `probeAnno` holding genomic position, index and gene association of probes on array.
`y` | Corresponds to argument `probeAnno` when calling the S4 method
`chrom` | character; the chromosome to visualize
`xlim` | start and end genomic coordinates on the chromosome to visualize
`ylim` | minimum and maximum probe intensities for the plot, if missing (default) set to `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.
`ylab` | character; label for the y-axis, passed on to the plotting function as `ylab`
`ipch` | plot character to use
`icex` | character expansion to use for plotting symbol
`ilwd` | line width of plotted data lines
`ilty` | line type of plotted data lines; passed on to `par(lty)`.
`gff` | data frame containing annotation for genomic feature to be used to further annotate the plot.
`featureExclude` | character vector specifying the feature types in the data.frame `gff` that should not be shown in the plot
`zeroLine` | logical; should a dashed horizontal line at y=0 be put into the plot?
`sampleLegend` | logical; should a sample legend be put into the plot?
`sampleLegendPos` | character; where to put the sample legend; one of ‘topleft’ (default), ‘bottomleft’, ‘topright’, or ‘bottomrigth’
`featureLegend` | logical; should a feature legend be put beneath the plot?
`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
`highlight` | optional list specifying a genomic region to be highlighted in the shown plot
`main` | optional main title for the plot; if not specified: the default is ‘Chromosome coordinate [bp]’
`...` | further parameters passed on to `grid.polyline` and `grid.points`

### Value

`invisible` list of probe positions (element `x`) and probe levels (element `y`) in the selected genomic region.

### Note

The S4 method is provided as a mere convenience wrapper.

When plotting a new ‘grid’ plot in an active x11 window that already contains a plot, remember to call `grid.newpage()` before.

### Author(s)

Joern Toedling

### See Also

`ExpressionSet-class`, `probeAnno-class`, `grid.points`, `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
      plot(exampleX, exProbeAnno, chrom="9",
           xlim=c(34318000,34321000), ylim=c(-2,4), gff=exGFF)

      ### this should give you the same result as:
      chipAlongChrom(exampleX, chrom="9", xlim=c(34318000,34321000),
                     ylim=c(-2,4), probeAnno=exProbeAnno, gff=exGFF)

[Package Ringo version 1.48.0 Index]