plotResults: A function for plotting quality indicators, including PCA...

View source: R/mrbin.R

plotResultsR Documentation

A function for plotting quality indicators, including PCA plots.

Description

This function plots boxplots (bin-wise and sample-wise) as visual quality indicators. It also performs PCA, then plots PC1 and PC2 and loading plots.

Usage

plotResults(mrbinResults, defineGroups = TRUE, process = TRUE, silent = FALSE)

Arguments

mrbinResults

An mrbin object

defineGroups

Should group membership be highlighted in PCA?

process

If set to FALSE, the file name will be extended by "Raw" to indicate that data has not been processed yet

silent

If set to TRUE, plots will be saved but not shown for the binning step for speed purposes

Value

None

Examples

mrbinResults<-mrbin(silent=TRUE,setDefault=FALSE,parameters=list(dimension="2D",
    binRegion=c(8,1,15,140),binwidth2D=0.2,binheight=4,solventRegion=c(5.5,4.2),
    PQNScaling="No",noiseRemoval="Yes",trimZeros="Yes",tryParallel=TRUE,
    fixNegatives="No",logTrafo="No",PCA="No",signal_to_noise2D=10,
    NMRfolders=c(system.file("extdata/1/12/pdata/10",package="mrbin"),
                 system.file("extdata/2/12/pdata/10",package="mrbin"))))
plotResults(mrbinResults)

mrbin documentation built on June 22, 2024, 9:39 a.m.