gene.strip {exonmap}R Documentation

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

Description

Takes a list of genes and an ExpressionSet object and generates a plot. Each row corresponds to a gene, X axis corresponds to position. By default each exon is ploted as a rectangle, coloured by expression (see below), and introns are ignored. Overlapping exons are plotted next to each other, if multiple probesets hit an exon they are stacked. Data are filtered to remove multiply targeted probesets. If there are no 'well-behaved' probesets hitting an exon it is drawn as a white rectangle.

If plot.introns is TRUE then introns are included in the plot, and position on the x-axis is relative to the start of the gene. Exons are drawn as rectangles in the border colour - default is black. Note that they will show up as verticle lines, if the gene is long and the data are compressed to fit into the space available for the plot. Each probe is represented by a circle (in the border colour; default is black) and a line which is coloured by expression.

Usage

gene.strip(X,data,gp1,gp2,plot.introns=FALSE,labels,type=c("mean-fc","min-fc","max-fc","min-tt","mean-int","median-int","min-int","max-int"),
           scale.to.gene=FALSE,palette=col.rd.bl,col.range=c(-5,5),use.only.wbex=TRUE,exclude.mt=TRUE,
           cex=0.5,xlab,ylab,border="black",plot=TRUE)

Arguments

X the Ensembl gene id of the gene to plot
data Expression data (should be an ExpressionSet). Used to colour the plot
gp1 indices into the expression data; group 1 for pairwise fold-change and t-test calculations
gp2 indices into the expression data; group 2 for pairwise fold-change and t-test calculations
plot.introns Changes style of the graph to show both exons and introns
labels Labels for the gene defaults to the Ensembl gene ID, the gene name and a '>' or '<' indicating whether the gene is on the forward or reverse strand
type The calculation used to generate the colouring
scale.to.gene If true, colouring is relative to the average expression for the gene
palette Colours used to represent expression
col.range Numerical extent of the colouring
use.only.wbex Ignore probesets that don't hit the genome in one place, within an exon
exclude.mt If use.only.wbex is FALSE then itron probesets are used if plot.introns=TRUE. exclude.mt will filter this list to remove probesets that hit the genome at multiple sites
cex character size
xlab x axis label
ylab y axis label
border colour to paint edges of exons and, if plot.introns is TRUE, probe locations
plot Just set up axes, don't plot whole graph. Useful because large graphs can take a long time to plot; this parameter makes it possible to check labels etc. are as expected.

Details

At its simplest, takes an ensembl gene id 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 into the chosen palette and using the resulting colour to paint the gene. The same is done for transcripts and exons. 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 fold change for the gene.

Note that for fold change calculations the number returned is (gp1 - gp2) i.e. if gp1 is more highly expressed than group 2, the result is positive. With default colouring, positive values are blue, negative, red.

Value

none

Author(s)

Crispin Miller

References

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

See Also

gene.legend

Examples

 
  ## Not run: 
     plot.gene("ENSG00000141510")
  
## End(Not run)

[Package exonmap version 1.0.07 Index]