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Last data update: 2014.03.03

R: Multi-dimensional scaling plots giving an overview of...

mdsPlot

R Documentation

Multi-dimensional scaling plots giving an overview of similarities and differences between samples.

Description

Multi-dimensional scaling (MDS) plots showing a 2-d projection of distances between samples.

Usage

mdsPlot(dat, numPositions = 1000, sampNames = NULL, sampGroups = NULL, xlim, ylim,
    pch = 1, pal = brewer.pal(8, "Dark2"), legendPos = "bottomleft",
    legendNCol, main = NULL)

Arguments

`dat`	An `RGChannelSet`, a `MethylSet` or a `matrix`. We either use the `getBeta` function to get Beta values (for the first two) or we assume the matrix contains Beta values.
`numPositions`	Use the `numPositions` genomic positions with the most methylation variability when calculating distance between samples.
`sampNames`	Optional sample names. See details.
`sampGroups`	Optional sample group labels. See details.
`xlim`	x-axis limits.
`ylim`	y-axis limits.
`pch`	Point type. See `par` for details.
`pal`	Color palette.
`legendPos`	The legend position. See `legend` for details.
`legendNCol`	The number of columns in the legend. See `legend` for details.
`main`	Plot title.

Details

Euclidean distance is calculated between samples using the numPositions most variable CpG positions. These distances are then projected into a 2-d plane using classical multidimensional scaling transformation.

Value

No return value. Plots are produced as a side-effect.

Author(s)

Martin Aryee aryee@jhu.edu.

References

I Borg, P Groenen. Modern Multidimensional Scaling: theory and applications (2nd ed.) New York: Springer-Verlag (2005) pp. 207-212. ISBN 0387948457.

http://en.wikipedia.org/wiki/Multidimensional_scaling

Examples

if (require(minfiData)) {

names <- pData(MsetEx)$Sample_Name
groups <- pData(MsetEx)$Sample_Group
mdsPlot(MsetEx, sampNames=names, sampGroups=groups)

}

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)

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> library(minfi)
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

Loading required package: Biobase
Welcome to Bioconductor

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

Loading required package: lattice
Loading required package: GenomicRanges
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

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

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
Loading required package: Biostrings
Loading required package: XVector
Loading required package: bumphunter
Loading required package: foreach
Loading required package: iterators
Loading required package: locfit
locfit 1.5-9.1 	 2013-03-22
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/minfi/mdsPlot.Rd_%03d_medium.png", width=480, height=480)
> ### Name: mdsPlot
> ### Title: Multi-dimensional scaling plots giving an overview of
> ###   similarities and differences between samples.
> ### Aliases: mdsPlot
> 
> ### ** Examples
> 
> if (require(minfiData)) {
+ 
+ names <- pData(MsetEx)$Sample_Name
+ groups <- pData(MsetEx)$Sample_Group
+ mdsPlot(MsetEx, sampNames=names, sampGroups=groups)
+ 
+ }
Loading required package: minfiData
Loading required package: IlluminaHumanMethylation450kmanifest
Loading required package: IlluminaHumanMethylation450kanno.ilmn12.hg19
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>