plotResults: A function for plotting quality indicators, including PCA...
In mrbin: Metabolomics Data Analysis Functions

plotResults

R 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.