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Last data update: 2014.03.03

R: Plot outlier locations

outlierplot

R Documentation

Plot outlier locations

Description

Function to plot where the outliers are located on a given array

Usage

outlierplot(BLData, array = 1, transFun = logGreenChannelTransform, outlierFun = illuminaOutlierMethod,n=3, wtsname=NULL, horizontal = TRUE, nSegments = NULL, lowOutlierCol = "blue", highOutlierCol = "pink", outlierPch = ".", main = "", ...)

Arguments

`BLData`	a `beadLevelData` object
`array`	the number of the array to plot
`transFun`	a function defining how to transform the data prior to calculating outliers
`outlierFun`	function that will identify outliers
`n`	an indicator of how extreme an observation must be (e.g. how many MADs from the median), to be passed to the function that will identify outliers
`wtsname`	column name of BLData object containing weights to feed to the outlier function
`horizontal`	if TRUE the longest edge of the array section will be on the x axis
`nSegments`	How many segments the section is divided into. If this argument is left as the default value (NULL) the code will attempt to extract this information from the relevant .sdf file. If it can't be found then the segments will not be indicated on the final plot.
`lowOutlierCol`	what colour to plot outliers below the median
`highOutlierCol`	what colour to plot outliers above the median
`outlierPch`	plotting character for the outliers
`main`	an optional title for the plot
`...`	additional arguments

Details

The function calls the specified outlier function to determine the outliers on the array and then plots their location. Points are coloured according the intensity of the bead is above or below the median for that bead-type.

Value

plot produced on current graphical device

Author(s)

Mark Dunning and Mike Smith

Examples


if(require(beadarrayExampleData)){

data(exampleBLData)
outlierplot(exampleBLData, array=1, horizontal = FALSE)


}

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 'license()' or 'licence()' for distribution details.

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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/outlierplot.Rd_%03d_medium.png", width=480, height=480)
> ### Name: outlierplot
> ### Title: Plot outlier locations
> ### Aliases: outlierplot
> 
> ### ** Examples
> 
> 
> if(require(beadarrayExampleData)){
+ 
+ data(exampleBLData)
+ outlierplot(exampleBLData, array=1, horizontal = FALSE)
+ 
+ 
+ }
Loading required package: beadarrayExampleData
22096  outliers found on the section
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>