alongChrom: A function for plotting expression data from an ExpressionSet...
In geneplotter: Graphics related functions for Bioconductor

Description Usage Arguments Details Author(s) Examples

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

   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",
   ...)

`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()

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.

Jeff Gentry

   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")

Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
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    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: lattice
Loading required package: annotate
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: XML
Loading required package: hgu95av2.db
Loading required package: org.Hs.eg.db


[1] "Warning: Not all requested genes are displayed."
[1] "Warning: Not all requested genes are displayed."
[1] "Warning: Not all requested genes are displayed."
[1] "Warning: Not all requested genes are displayed."