annotationDiagnosticPlots-peakPantheRAnnotation-method: Generate fit diagnostic plots

In phenomecentre/peakPantheR: Peak Picking and Annotation of High Resolution Experiments

Generate fit diagnostic plots

Description

Generate fit diagnostic plots for each ROI: EICFit the raw data and detected feature fit, rtPeakwidthVert detected peaks retention time apex and peakwidth (vertical and no run order), rtPeakwidthHorzRunOrder detected peaks retention time apex and peakwidth by run order, mzPeakwidthHorzRunOrder detected peaks m/z apex and peakwidth by run order, areaRunOrder detected peaks area by run order, rtHistogram histogram of detected peaks retention time, mzHistogram histogram of detected peaks m/z, areaHistogram histogram of detected peaks area.

Usage

## S4 method for signature 'peakPantheRAnnotation'
annotationDiagnosticPlots(
    object,
    sampleColour,
    sampling,
    verbose
)

Arguments

object	(peakPantheRAnnotation) Annotated peakPantheRAnnotation object
sampleColour	(str) NULL or vector colour for each sample
sampling	(int) Number of points to employ when plotting fittedCurve
verbose	(bool) if TRUE message the plot generation progress

Value

A list (one list per compound) of diagnostic plots: result[[i]]$EICFit, result[[i]]$rtPeakwidthVert, result[[i]]$rtPeakwidthHorzRunOrder, result[[i]]$mzPeakwidthHorzRunOrder, result[[i]]$areaRunOrder, result[[i]]$rtHistogram, result[[i]]$mzHistogram, result[[i]]$areaHistogram, result[[i]]$title

Examples

if(requireNamespace('faahKO')){
## Initialise a peakPantheRAnnotation object with 3 samples and 2 targeted
## compounds

# Paths to spectra files
library(faahKO)
spectraPaths <- c(system.file('cdf/KO/ko15.CDF', package = 'faahKO'),
                    system.file('cdf/KO/ko16.CDF', package = 'faahKO'),
                    system.file('cdf/KO/ko18.CDF', package = 'faahKO'))

# targetFeatTable
targetFeatTable <- data.frame(matrix(vector(), 2, 8, dimnames=list(c(),
                    c('cpdID','cpdName','rtMin','rt','rtMax','mzMin','mz',
                    'mzMax'))), stringsAsFactors=FALSE)
targetFeatTable[1,] <- c('ID-1', 'Cpd 1', 3310., 3344.888, 3390., 522.194778,
                        522.2, 522.205222)
targetFeatTable[2,] <- c('ID-2', 'Cpd 2', 3280., 3385.577, 3440., 496.195038,
                        496.2, 496.204962)
targetFeatTable[,c(3:8)] <- vapply(targetFeatTable[,c(3:8)], as.numeric,
                                    FUN.VALUE=numeric(2))

emptyAnnotation <- peakPantheRAnnotation(spectraPaths=spectraPaths,
                                        targetFeatTable=targetFeatTable)

annotationDiagnosticPlots(emptyAnnotation)
# Warning: the object has not been annotated, return an empty diagnostic plot
# list
# [[1]]
# NULL
# [[2]]
# NULL
}

phenomecentre/peakPantheR documentation built on Feb. 29, 2024, 9:07 p.m.