alongChrom {geneplotter} | R Documentation

## A function for plotting expression data from an ExpressionSet for a given chromosome.

### Description

Given a particular ExpressionSet object, a chromLocation object, and a chromosome name, will plot selected ExpressionSet data using various methods.

### Usage

       alongChrom(eSet, chrom, specChrom,  xlim, whichGenes,
       plotFormat=c("cumulative", "local","image"),
       xloc=c("equispaced", "physical"),
       scale=c("none","zscale","rankscale","rangescale","zrobustscale"),
       geneSymbols=FALSE, byStrand=FALSE, colors="red", lty=1, type="S",
       ...)

### Arguments

`eSet` | The ExpressionSet object to be used.
`chrom` | The desired chromosome.
`specChrom` | An object of type chromLocation for the species being represented.
`xlim` | A pair of values - either character or integer, which will denote the range of genes to display (based on base pair: either directly in the case of integers, or using the locations of the named genes if character). If not supplied, the entire chromosome is used.
`whichGenes` | If supplied, will limit the displayed genes to the ones provided in this vector.
`xloc` | Determines whether the X axis points (gene names) will be displayed according to their relative position on the chromosome (physical), or spaced evenly (equispaced). Default is equispaced.
`plotFormat` | Determines the method which to plot the data.
`scale` | Determines what method of scaling will be applied to the data. Default is none.
`geneSymbols` | Notes whether to use Affy IDs or Gene Symbols, default is Affy IDs
`byStrand` | Determines whether to show the entire plot at once, or a split plot by strands. Default is a singular plot
`lty` | A vector of line types, which will be cycled.
`type` | Plot type, from par. Defaults to "S".
`colors` | A vector of colors for the plots, which will be cycled.
`...` | Any remaining graphics commands may be passed along as per plot()

### Details

The genes on the chromosome of interest are extracted from the `chromLocation` object passed in, which are then intersected with the genes listed in the ExpressionSet. These remaining genes will then be plotted according to the `plotFormat` argument. If `image` is specified, an image plot is created showing the expression levels of the samples by gene, using a colour map to denote the levels. If `cumulative` is chosen, the cumulative expression level is plotted against the genes for each sample. Likewise, if `local` is used, the raw data is plotted for each sample against the genes using a boxplot format.

Not all parameters are honored for all plotformats. `xloc`, `lty`, and `type` are only used with the `cumulative` plotformat.

### Author(s)

Jeff Gentry

### Examples

       data(sample.ExpressionSet)
       ## A bit of a hack to not have a package dependency on hgu95av2
       ## but need to fiddle w/ the warn level to not fail the example anyways.
       curWarn <- options(warn=0)
       on.exit(options(curWarn), add=TRUE)
       if (require("hgu95av2.db")) {
          z <- buildChromLocation("hgu95av2")
          lty <- c(1, 2, 3, 4, 5)
          cols <- c("red", "green", "blue", "orange", "magenta", "black")
          cols <- cols[sample.ExpressionSet$type]
          if (interactive()) {
             par(ask=TRUE)
          }

          ## Here we're using xlim to denote a physical region to display
          xlim <- c(87511280,127717880)
          for (xl in c("equispaced", "physical"))
            for (sc in c("none","rangescale"))
            {
               alongChrom(sample.ExpressionSet, "1", z, xlim=xlim, xloc=xl,
                  plotFormat="cumulative", scale=sc,lty=lty, colors=cols)
            }

         ## Here we're looking for specific genes
         which <- c("31540_at","31583_at", "31508_at", "31529_at", "31439_f_at",
                   "31729_at")
         ## Gene "31529_at" does not exist in the current set of genes,
         ## here it demonstrates how genes not available are dropped.
          for (xl in c("equispaced", "physical"))
            for (sc in c("none","rangescale"))
            {
                alongChrom(sample.ExpressionSet, "1", z, which=which, xloc=xl,
                   plotFormat="cumulative", scale=sc,lty=lty, col=cols)
             }

          ## Do an image plot
          for (bs in c(TRUE,FALSE))
             alongChrom(sample.ExpressionSet, "1",z, xlim=xlim, plotFormat="image",
                       scale="zscale", byStrand=bs)

          ## A boxplot
          for (st in c(TRUE,FALSE))
             alongChrom(sample.ExpressionSet, "1", z, plotFormat="local",
                        colors=cols, byStrand=st)
        } else print("Example can not be run without the hgu95av2 data package")

[Package geneplotter version 1.66.0 Index]