beadarray (version 2.22.2)

outlierplot: 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

Value

plot produced on current graphical device

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.

Examples

if(require(beadarrayExampleData)){

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


}