Plots the correlation in gene expression between more than 2 samples

Description

Plots a correlation matrix in gene expression between two samples. Each dot represents a gene, and the dots have a density-dependent coloring.

Usage

plotCombMultSamples(exprsMatrix, ...)

Arguments

Author(s)

Willem Talloen

See Also

plotComb2Samples

Examples

if (require(ALL)){
  data(ALL, package = "ALL")
  ALL <- addGeneInfo(ALL)

  plotCombMultSamples(exprs(ALL)[,c("84004", "11002", "01003")])
}

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.
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Type 'license()' or 'licence()' for distribution details.

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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(a4Base)
Loading required package: grid
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")'.

Loading required package: AnnotationDbi
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Attaching package: 'S4Vectors'

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Loading required package: annaffy
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Loading required package: KEGG.db

KEGG.db contains mappings based on older data because the original
  resource was removed from the the public domain before the most
  recent update was produced. This package should now be considered
  deprecated and future versions of Bioconductor may not have it
  available.  Users who want more current data are encouraged to look
  at the KEGGREST or reactome.db packages

Loading required package: mpm
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Attaching package: 'MASS'

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    select

Loading required package: KernSmooth
KernSmooth 2.23 loaded
Copyright M. P. Wand 1997-2009

mpm version 1.0-22

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Attaching package: 'genefilter'

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Attaching package: 'limma'

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Attaching package: 'Matrix'

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Attaching package: 'a4Core'

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Loading required package: gplots

Attaching package: 'gplots'

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The following object is masked from 'package:S4Vectors':

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

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a4Base version 1.20.0

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/a4Base/plotCombMultSamples.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plotCombMultSamples
> ### Title: Plots the correlation in gene expression between more than 2
> ###   samples
> ### Aliases: plotCombMultSamples
> 
> ### ** Examples
> 
> if (require(ALL)){
+   data(ALL, package = "ALL")
+   ALL <- addGeneInfo(ALL)
+ 
+   plotCombMultSamples(exprs(ALL)[,c("84004", "11002", "01003")])
+ }
Loading required package: ALL
Loading required package: hgu95av2.db
Loading required package: org.Hs.eg.db


Warning messages:
1: In plot.xy(xy.coords(x, y), type = type, ...) :
  "axes" is not a graphical parameter
2: In plot.xy(xy.coords(x, y), type = type, ...) :
  "axes" is not a graphical parameter
3: In plot.xy(xy.coords(x, y), type = type, ...) :
  "axes" is not a graphical parameter
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>