plotGene {exonmap}R Documentation

Use the X:MAP database to find annotated gene structure and generate a plot

Description

Draws a plot of a gene's structure, possibly coloured by expression data, similar to those shown in the X:Map genome browser.

Usage

plotGene(x, data, gps, group, scale.to.gene = FALSE, 
    type = c("mean-int", "median-int", "mean-fc", "median-fc", "splicing-index"), 
    use.symbol = TRUE, use.mt = FALSE, 
    probes.min = 4, f = ps.value, f.extra.params, 
    col = col.rd.bl, col.range, col.f = value.to.colour,
    main, xlab, ylab, xlim, ylim,
    border.col = "#aaaaaa",no.data.col = "white", text.col="black",text.bg="white",
    exon.borders,
    pad=0.1,transcript.height=0.9,show.legend=TRUE)

col.rd.bl

Arguments

x the Ensembl gene id of the gene to plot
data Expression data (should be a matrix or ExpressionSet). If present, used to colour the plot
gps Either a list of groups by which to collect the expression data when calculating, for example, fold change or mean intensities, or, if group is specified, the names of items in one of the columns in pData(x). See details.
group If specified, then the column in pData(x) to use when defining the groups of arrays to compare. See details.
scale.to.gene If TRUE, then mean-center each plot around zero.
type The type of calculatin used to create the data for the plot. See details.
use.symbol If TRUE then label by the gene symbol, if FALSE, the gene name.
use.mt If TRUE then include multitarget probesets. See select.probewise and exclude.probewise for details on how the filtering is done.
probes.min The minimum number of probes within a probeset that must match to an exon before it is incorporated in the plot.
f The function used to map between the expression data and a colour in col. By default, this is ps.value.
f.extra.params Any extra parameters that need to be passed through to f. This is only necessary if supplying an alternative function for computing the colourings.
col A vector containing the colours to use when colouring the plot by expression data. col.rd.bl is used by default.
col.range A range specifying the extents of the colour palette. Expression data are turned into a value for each probeset (how this is done is defined by type) and then mapped into the colour vector col. col.range specifies the value corresponding to the first and last entry in the colour palette; values outside this range are mapped to the extremes. By default the ranges are c(-5,5) for fold change plots and c(0,16) for intensity.
col.f Function used to map the expression summary data generated by f to a colour in col. Not normally required; might be used for a non-linear scale, for example.
main Plot title.
xlab X axis label. Overrides use.symbol.
ylab Y axis label.
xlim Range of values to plot on the x axis.
ylim Height of y-axis. By default this is just big enough to fit the gene.
border.col Colour to use for gene, transcript and exon edges.
no.data.col Colour to plot exons with no matching probeset after filtering using probes.min and use.mt.
text.col Colour to label genes and transcripts.
text.bg Label background colour for the gene label.
exon.borders If TRUE then draw a border around exons.
pad Vertical space to leave between each element of the plot. Character height is adjusted to be the same as pad
transcript.height Height of each transcript. With defaults, each gene is (transcript.height + pad) * N + 3 * pad high
show.legend If TRUE, show a colour bar as a legend in the margin of the plot.

Details

At its simplest, takes an Ensembl gene name and plots the location and structure of the gene. If data, gp1, and gp2 are specified, then colours the gene according to the expression data. By default, this is done by calculating the mean fold change for all the well behaved exon probes (i.e. those that only hit the genome, once, in an exon in the gene of interest), mapping this value to a colour and using this to paint each exon in the gene. The same is done for transcripts and genes. Other methods of colouring are specified by type, and should be self-explanatory. See the vignette for more details. If scale.to.gene is TRUE, then fold-changes (or intensities, depending on the value of type) are calculated relative to the mean fold change for the gene. Exons for which no matching probesets are found are drawn with a black border and annotated with an 'x'.

Groups of arrays can be specified in two ways, depending on whether groups is supplied. If it is, then it should represent the name of a column in the ExpressionSet's pData object, and gps should be a list of levels in this factor defining the groups of arrays. So for example, ...,group="group",gps=c("a","b"),... will define two groups of arrays, one for each cell line, as defined by the "group" column in the expression set's pData object.

Alternatively, if groups is not supplied, gps should be a list of numeric vectors, each defining the indices of a set of arrays. For example, ...,gps=list(a=1:3,b=4:6),... would define two groups, called "a" and "b", each with three arrays in it.

Note that for fold change calculations the number returned is gps[1] -gps[2] i.e. if gp[1] is more highly expressed than group 2, the result is positive. With default colouring, positive values are blue, negative, red.

Colouring can be changed by supplying an alternate palette to the default (col.rd.bl), and alternate mappings between values and colours can be generated by supplying a different function via col.f. See value.to.colour for more details.

Value

none

Author(s)

Crispin Miller

References

http://bioinformatics.picr.man.ac.uk/

See Also

gene.legend gene.strip gene.graph mappings filters details

Examples

 
  if(interactive()) {   
   xmapConnect()
   data(exonmap)
   par(mfrow=c(3,1))
   plotGene("ENSG00000141510",x.rma,gps=list(1:3,4:6),type="mean-fc")
   plotGene("ENSG00000141510",x.rma,gps=c("a","b"),group="group",type="mean-fc")
   plotGene("ENSG00000141510",x.rma,gps=list(1:3),type="mean-int",col=heat.colors(16))
   plotGene("ENSG00000141510",x.rma,gps=list(4:6),type="mean-int",col=heat.colors(16))
  }

[Package exonmap version 2.0.03 Index]