outputAnnotationDiagnostic-peakPantheRAnnotation-method: Save to disk the annotation parameters as CSV and a...

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

Save to disk the annotation parameters as CSV and a diagnostic plot per fitted compound

Description

Save to disk the annotation parameters as CSV (as generated by outputAnnotationParamsCSV()) and a diagnostic plot per fitted compound (as generated by annotationDiagnosticMultiplot()) if savePlots is TRUE

Usage

## S4 method for signature 'peakPantheRAnnotation'
outputAnnotationDiagnostic(
    object,
    saveFolder,
    savePlots = TRUE,
    sampleColour = NULL,
    verbose = TRUE,
    ncores = 0,
    svgPlot = FALSE,
    ...
)

Arguments

object	(peakPantheRAnnotation) Annotated peakPantheRAnnotation object
saveFolder	(str) Path of folder where annotationParameters_summary.csv and plots will be saved
savePlots	(bool) If TRUE save a diagnostic plot for each compound
sampleColour	(str) NULL or vector colour for each sample
verbose	(bool) If TRUE message progress
ncores	(int) Number of cores to use to save plots in parallel
svgPlot	(bool) If TRUE save plots as 'svg', otherwise as 'png'
...	Additional parameters for plotting i.e. sampling for the number of points to employ when plotting fittedCurve

Value

None

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)

# Calculate annotation
annotation <- peakPantheR_parallelAnnotation(emptyAnnotation, ncores=0,
                                getAcquTime=FALSE, verbose=FALSE)$annotation

# temporary location
savePath1       <- tempdir()
outputAnnotationDiagnostic(annotation, saveFolder=savePath1, savePlots=FALSE,
                            verbose=TRUE)
}

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