plot.gene {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 that found on the X:MAP website

Usage

plot.gene(x,data,gp1,gp2,xlim,ylim,tick.labels=T,
          border="black",
          show.probes=T,probe.colour="black",show.mt=T,mt.colour="grey",
          type=c("mean-fc","min-fc","max-fc","min-tt","mean-int","median-int","min-int","max-int"),
          use.only.wbex=T,palette=col.rd.bl,col.range,scale.to.gene=F,draw.exon.border=T,colour.transcript=F,
          draw.legend=T,cex=0.5,...)
col.rd.bl

Arguments

x the Ensembl gene id of the gene to plot
data Expression data (should be an ExpressionSet). If present, 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
xlim chromosomal coordinates for the plot. If missing defaults to the position of the gene
ylim height of the plot
tick.labels label ticks?
border colour to draw gene/transcript/exon edges and text
show.probes draw individual probes?
probe.colour colour for well-behaving probes
show.mt draw multiply targeted probes
mt.colour colour to draw multiply targeted probes
type how to colour by expression data
use.only.wbex only use well behaving exon probes for expression colouring
palette colour scheme for expression colouring
col.range min aand maximum values (e.g. fold-change) to map to the colour palette
scale.to.gene pre-scale exon colours to the value for the gene before plotting
draw.exon.border draw an edge round the exons?
colour.transcript colour individual transcripts by expression?
draw.legend add a colour bar to the plot?
cex character expansion
... additional parameters to pass through to plot

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]