Description Usage Arguments Value Examples
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.
1 2 3 4 5 6 7 | ## S4 method for signature 'peakPantheRAnnotation'
annotationDiagnosticPlots(
object,
sampleColour,
sampling,
verbose
)
|
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 |
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
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 | 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
}
|
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