outputAnnotationDiagnostic,peakPantheRAnnotation-method {peakPantheR} | R Documentation |
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 signature 'peakPantheRAnnotation' outputAnnotationDiagnostic( object, saveFolder, savePlots = TRUE, sampleColour = NULL, verbose = TRUE, ncores = 0, ... )
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. |
None
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) }