This function allows one to create scatterplots of gene pairs that may
be involved in recurrent gene fusion in cancer.
Usage
scatterPlotCopa(copa, idx, lib = 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.
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.
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/scatterPlotCopa.Rd_%03d_medium.png", width=480, height=480)
> ### Name: scatterPlotCopa
> ### Title: Create scatterplots of interesting gene pairs
> ### Aliases: scatterPlotCopa
> ### Keywords: hplot
>
> ### ** Examples
>
> #if(interactive()){
> library(Biobase)
> data(sample.ExpressionSet)
> cl <- abs(3 - as.numeric(pData(sample.ExpressionSet)[,2]))
> tmp <- copa(sample.ExpressionSet, cl)
> scatterPlotCopa(tmp, 1)
> #}
>
>
>
>
>
> dev.off()
null device
1
>