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Last data update: 2014.03.03

R: Plot the color bias of Illumina Infinium Methylation data in...

plotColorBias2D

R Documentation

Plot the color bias of Illumina Infinium Methylation data in two dimensions

Description

Plot the color bias (red and green channel) of Illumina Infinium Methylation data of one selected sample in two dimensions (methylated and unmethylated probe intensities)

Usage

plotColorBias2D(methyLumiM, selSample = 1, combineMode = F, layoutRatioWidth = c(0.75, 0.25), layoutRatioHeight = c(0.25, 0.75), margins = c(5, 5, 2, 2), cex = 1.25, logMode = TRUE, subset = NULL, ...)

Arguments

`methyLumiM`	MethyLumiM-class object or eSet-class object, which include methylated and unmethylated probe intensities
`selSample`	The index of sample name of the selected sample to plot color bias
`combineMode`	Whether combine two color channels together and plot as one color
`layoutRatioWidth`	the plot figure ratio between scatter plot and density plot
`layoutRatioHeight`	the plot figure ratio between scatter plot and density plot
`margins`	margin of the plot
`cex`	A numerical value giving the amount by which plotting text and symbols should be magnified relative to the default. See `par`
`logMode`	Whether plot the intensities in log-scale
`subset`	plot subset of randomly selected rows. All data will be plotted if it is NULL.
`...`	other parameters used by `plot`

Details

The function basically plots the probe intensities in 2-dimension (methylated vs unmethylated), and colors the dots in Red and Green based on their color channel information. The related density plot will also be plotted at the right and top of the scatter plot.

Value

Invisibly return TRUE if plot successfully.

Author(s)

Pan DU

Examples

data(example.lumiMethy)
# plot in 2D plot of one selected sample
plotColorBias2D(example.lumiMethy, selSample = 1)

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(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/plotColorBias2D.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plotColorBias2D
> ### Title: Plot the color bias of Illumina Infinium Methylation data in two
> ###   dimensions
> ### Aliases: plotColorBias2D
> ### Keywords: methods hplot
> 
> ### ** Examples
> 
> data(example.lumiMethy)
> # plot in 2D plot of one selected sample
> plotColorBias2D(example.lumiMethy, selSample = 1)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>