plotCopa: Plot Gene Pairs fom the Results of Running copa
In copa: Functions to perform cancer outlier profile analysis.

Description Usage Arguments Details Value Author(s) References Examples

View source: R/copa.R

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

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

`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`

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.).

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

James W. MacDonald

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

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"))
}