plotSegmentationHeatmap {tilingArray} | R Documentation

## Plot a heatmap diagram for a region along a chromosome

### Description

Plot a heatmap diagram for a region along a chromosome

### Usage

    plotSegmentationHeatmap(dat, xlim, ylab, rowNames,
                            chr=1, strand="+", vpr, colors,
                            colHeatmap=colorRamp(brewer.pal(9, "YlGnBu")),
                            showConfidenceIntervals=TRUE,
                            just=c("left","centre"),
                            main,makeRasterImage = TRUE, ...)

### Arguments

`dat` | list containing data to be plotted (see Details section below for particulars).
`xlim` | integer vector of length 2 with start and end coordinates (in bases) for plotting.
`ylab` | character scalar specifying y-axis label.
`rowNames` | character vector specifying a name for each row in the heatmap plot.
`chr` | integer of length 1 indicating the chromosome to plot (defaults to 1).
`strand` | character scalar which should be set to either `+` or `-` to indicate which strand of DNA to plot the intensity values from (defaults to "+").
`vpr` | which viewport to plot the figure in. If this function is called directly by the user this argument should be left missing.
`colors` | named character vector, optional. If missing, a default color scheme is used: `c("+"="#00441b", "-"="#081d58", "duplicated"="grey", "cp"="#101010", "highlight"="red", "threshold"="grey")`, where the first three elements refer to colors of data points and the last three to those of lines in the plot.
`colHeatmap` | function describing color scheme for the heatmap plot (defaults to `YlGnBu` from RColorBrewer package).
`showConfidenceIntervals` | logical scalar indicating whether confidence intervals for each change-point are to be plotted (only available once segmentation has occurred).
`just` | character vector specifying the justification of the supplied values to the given coordinates; setting the first entry to "left" indicates that the supplied x-coordinates are the start positions of the probes, change this to "centre" if the x-coordinates are the probe middle positions. Usually the second entry should be "centre" (see `grid.rect`)
`main` | character vector specifying plot title.
`makeRasterImage` | logical scalar indicating whether to plot the heatmap image by the grid.raster (see `grid.raster`) or the grid.rect (see `grid.rect`) function in grid package.The default is to generate raster image, as it can be displayed much faster with a relatively smaller file size.
`...` | additional arguments.

### Details

This function is called by `plotAlongChrom` if the argument `what` is set to `heatmap`. Although this function can be called directly by the user, this is not recommended. The `dat` list contains the following items:

`x`

  x-coordinates (in bases) along chromosome

`y`

  intensity matrix of probes along chromosome

`flag`

  indicates probe uniqueness in the genome. Possibilities are 3: multiple perfect matches, 2: has no PM but one or more near-matches, 1: has exactly one PM and some near-matches in the genome, 0: has exactly one PM and no near-matches.

`extras`

  (optional) matrix of additional values (such as test-statistics/p-values) to be plotted

### Author(s)

Wolfgang Huber <huber@ebi.ac.uk>

### Examples

      data(segnf)
      data(gffSub)
      nmLabel = colnames(segnf$"1.+"@y)
      plotAlongChrom(segnf,chr=1,coord=c(35000,50000),what="heatmap",
      		gff=gffSub,rowNamesHeatmap=nmLabel) ##using raster image

[Package tilingArray version 1.66.0 Index]