plot.gene.graph {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, with a line graph showing expression over the gene's length for two sets of samples

Usage


plot.gene.graph(x,data,gp1,gp2,xlim,ylim,
                border="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"),
                palette=col.rd.bl,col.range=c(-5,5),use.only.wb=T,scale.to.gene=F,
                gp1.col="orange",
                gp2.col="red",
                draw.exon.border=T,exon.height=0.05,draw.legend=T,cex=0.5,xlab,ylab="",...)

Arguments

x The name of the gene to plot
data ExpressionSet containing expression data to map to gene
gp1 indices into the expression set for the first replicate group
gp2 indices into the expression set for the second replicate group
xlim range specifying position on the gene's chromosome to plot. Defaults to the location of the gene
ylim range specifying y axis extent
border colour for probesets exon borders etc.
show.mt plot probesets that hit the genome more than once
mt.colour colour to draw mt probesets
type how to summarize data for thhe replicate groups
palette vector of colours to use to colour the exons
col.range range specifying the numeric extent of the colouring
use.only.wb only use well behaving probesets to calculate the exon summaries
scale.to.gene calculate the summary value for the entire gene (e.g. mean fold change, mean intensity, ...) and scale all values relative to that before plotting
gp1.col group 1 colour
gp2.col group 2 colour
draw.exon.border draw a box round the exons?
exon.height how high to draw the exons
draw.legend add a legend to the plot?
cex label text expansion
xlab x axis label
ylab y axis label
... extra parameters to pass through to plot

Details

At its simplest, takes an ensemble gene id and plots the location of the gene and its exons. Data, gp1, and gp2 are used to colour the exons according to the expression data, and to draw line plots for each of the two groups. 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 exon. At the same time a line graph is produced for the individual probesets. 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 that 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

plot.gene

Examples

 
  ## Not run: 
     plot.gene.graph("ENSG00000141510",x.rma,1:3,4:6)
  
## End(Not run)

[Package exonmap version 1.0.07 Index]