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Last data update: 2014.03.03

R: Plotting the intensities of selected beads on a section

beadIntensityPlots

R Documentation

Plotting the intensities of selected beads on a section

Description

The function will plot the intensities of selected beads on a specified array

Usage

plotBeadIntensities(BLData, array = 1, BeadIDs, transFun = logGreenChannelTransform, cols = NULL, ...)

Arguments

`BLData`	a `beadLevelData` object
`array`	numeric specifying which array to plot the intensities from
`BeadIDs`	what ArrayAddress IDs to be plotted
`transFun`	function specifying what transformation to be applied to the `beadLevelData` prior to plotting
`cols`	a vector of colours to be used to plot each ID. If NULL the `rainbow` function is used to generate colours.
`...`	other argument that may be passed along to plot.

Details

The function will take all data from the specified section, apply the transformation (the default is to do log2) and then find the subset of beads that have the specified ID. These IDs should match the numeric ArrayAddress IDs that are stored in the beadLevelData object.

Value

Plot is produced on current graphical device.

Author(s)

Mark Dunning

Examples


if(require(beadarrayExampleData)){


data(exampleBLData)

randIDs = sample(getBeadData(exampleBLData, array=1, what="ProbeID"),10)

plotBeadIntensities(exampleBLData, array=1, BeadIDs = randIDs)

}

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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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(beadarray)
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: ggplot2
Welcome to beadarray version 2.22.2
beadarray versions >= 2.0.0 are substantial updates from beadarray 1.16.0 and earlier. Please see package vignette for details
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/beadarray/plotBeadIntensities.Rd_%03d_medium.png", width=480, height=480)
> ### Name: beadIntensityPlots
> ### Title: Plotting the intensities of selected beads on a section
> ### Aliases: plotBeadIntensities genericBeadIntensityPlot
> ### Keywords: hplots
> 
> ### ** Examples
> 
> 
> if(require(beadarrayExampleData)){
+ 
+ 
+ data(exampleBLData)
+ 
+ randIDs = sample(getBeadData(exampleBLData, array=1, what="ProbeID"),10)
+ 
+ plotBeadIntensities(exampleBLData, array=1, BeadIDs = randIDs)
+ 
+ }
Loading required package: beadarrayExampleData
> 
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>