Last data update: 2014.03.03

R: Pair plot of an ExpressionSet object
pairs-methodsR Documentation

Pair plot of an ExpressionSet object


Creating pairs plot of sample intensities in an ExpressionSet object


## S4 method for signature 'ExpressionSet'
pairs(x, ..., smoothScatter = FALSE, logMode = TRUE, subset = 5000, fold=2, dotColor=1, 
	highlight = NULL, highlightColor = 2, main = NULL, checkTransform = TRUE)



a ExpressionSet object


optional arguments to pairs.


whether use smoothScatter function to plot points


whether plot the data in log2 scale


subset of rows used to plot. It can be an index vector, or the length of a random subset


The fold-change threshold used to estimate the number of probes having high fold-changes


color of points in the scatter plot


the subset dots need to be highlighted


the color for those highlighted dots


title of the plot


whether to check the data is log2-transformed or not


To increase the plot efficiency, by default, we only plot RANDOMLY selected subset of points (based on parameter "subset"). If users want to plot all the points, they can set the parameter "subset = NULL". When smoothScatter is set as TRUE, the subsetting will be suppressed because smoothScatter function has good plot efficiency for large number of points.

See Also

LumiBatch-class, pairs


## load example data


pairs(example.lumi, smoothScatter=TRUE)


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> library(lumi)
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,, cbind, colnames,, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax,, pmin,, 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")'.

Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/lumi/pairs-methods.Rd_%03d_medium.png", width=480, height=480)
> ### Name: pairs-methods
> ### Title: Pair plot of an ExpressionSet object
> ### Aliases: pairs-methods pairs.ExpressionSet pairs,ExpressionSet-method
> ### Keywords: methods hplot
> ### ** Examples
> ## load example data
> data(example.lumi)
> pairs(example.lumi)
> pairs(example.lumi, smoothScatter=TRUE)
null device