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

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

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

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

...

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)
}
#> Polarity can not be extracted from netCDF files, please set manually the polarity with the 'polarity' method.
#> Polarity can not be extracted from netCDF files, please set manually the polarity with the 'polarity' method.
#> Polarity can not be extracted from netCDF files, please set manually the polarity with the 'polarity' method.
#> Annotation parameters saved at C:\Temp\RtmpOQUVbX/annotationParameters_summary.csv