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Last data update: 2014.03.03

R: Plot Gene Pairs fom the Results of Running copa

plotCopa

R Documentation

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`

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.).

Value

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

Author(s)

James W. MacDonald

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"))
}

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(copa)
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/copa/plotCopa.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plotCopa
> ### Title: Plot Gene Pairs fom the Results of Running copa
> ### Aliases: plotCopa
> ### Keywords: hplot
> 
> ### ** 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"))
> #}
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>