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Last data update: 2014.03.03

R: Pair plot of an ExpressionSet object

pairs-methods

R Documentation

Pair plot of an ExpressionSet object

Description

Creating pairs plot of sample intensities in an ExpressionSet object

Usage

## 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)

Arguments

`x`	a `ExpressionSet` object
`...`	optional arguments to `pairs`.
`smoothScatter`	whether use `smoothScatter` function to plot points
`logMode`	whether plot the data in log2 scale
`subset`	subset of rows used to plot. It can be an index vector, or the length of a random subset
`fold`	The fold-change threshold used to estimate the number of probes having high fold-changes
`dotColor`	color of points in the scatter plot
`highlight`	the subset dots need to be highlighted
`highlightColor`	the color for those highlighted dots
`main`	title of the plot
`checkTransform`	whether to check the data is log2-transformed or not

Details

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.

Examples

## load example data
data(example.lumi)

pairs(example.lumi)

pairs(example.lumi, smoothScatter=TRUE)

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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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,
    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")'.

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)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>