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Last data update: 2014.03.03

R: Visualization of a result of the DEXUS algorithm.

plot	R Documentation

Visualization of a result of the DEXUS algorithm.

Description

Plots a heatmap of the log read counts of the top ranked genes or of selected genes.

Arguments

`x`	An instance of "CNVDetectionResult"
`idx`	The indices or the transcript names of the transcripts that should be visualized as heatmap.
`cexSamples`	Size of the column labels, i.e. the samples.
`cexGenes`	Size of the row labels, i.e. the transcripts.
`newColNames`	renames the samples.
`type`	Mark the samples, that do not belong to the major class by crosses ("crosses"), or boxes ("boxes").

Value

Generates a heatmap of the expression values of the top-ranked transcripts.

Author(s)

Guenter Klambauer klambauer@bioinf.jku.at and Thomas Unterthiner unterthiner@bioinf.jku.at

Examples

data(dexus)
r <- dexus(countsBottomly[1:100, ])
plot(r)

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(dexus)
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


Attaching package: 'dexus'

The following object is masked from 'package:BiocGenerics':

    sizeFactors

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/dexus/plot.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plot
> ### Title: Visualization of a result of the DEXUS algorithm.
> ### Aliases: plot
> 
> ### ** Examples
> 
> data(dexus)
> r <- dexus(countsBottomly[1:100, ])
Filtered out 5 % of the genes due to low counts
Unsupervised mode.
> plot(r)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>