outputAnnotationDiagnostic,peakPantheRAnnotation-method {peakPantheR} | R Documentation

## 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,
        ...
    )

### 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)
    }

[Package peakPantheR version 1.4.0 Index]