copa (version 1.40.0)

plotCopa: Plot Gene Pairs fom the Results of Running copa

Description

This function can be used to visualize pairs of genes that may be involved in recurrent gene fusion in cancer.

Usage

plotCopa(copa, idx, lib = NULL,  sort = TRUE, col = NULL, legend = NULL)

Arguments

copa

An object of class 'copa', resulting from a call to the copa function.

idx

A numeric vector listing the gene pairs to plot (e.g., idx = 1:3 will plot the first three gene pairs).

lib

If the underlying data are Affymetrix expression values, one can specify an annotation package and the plot labels will be extracted from the xxxSYMBOL environment. If NULL, the row.names of the gene expression matrix will be used.

sort

Boolean. Should the data be sorted before plotting? Defaults to TRUE.

col

A vector of color names or numbers to be used for coloring the different samples in the resulting barplot.

legend

A vector of terms describing the two sample types (e.g., 'Normal' and 'Tumor'). Defaults to NULL

Value

This function is called solely for outputting plots. No values are returned.

Details

Note that this function will output all the gene pairs in the idx vector without pausing. This can be controlled by either setting par(ask = TRUE), or by redirecting the output to a file (using e.g., pdf, ps, etc.).

References

Tomlins, SA, et al. Recurrent fusion of TMPRSS2 and ETS transcription factor genes in prostate cancer. Science. 2005 Oct 28;310(5748):644-8.

Examples

if(interactive()){
library(Biobase)
data(sample.ExpressionSet)
cl <- abs(3 - as.numeric(pData(sample.ExpressionSet)[,2]))
tmp <- copa(sample.ExpressionSet, cl)
plotCopa(tmp, 1, col = c("red", "blue"))
}