annotationDiagnosticPlots,peakPantheRAnnotation-method {peakPantheR} | R Documentation

## Generate fit diagnostic plots

### Description

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.

### Usage

    ## S4 method for signature 'peakPantheRAnnotation'
    annotationDiagnosticPlots(
        object,
        sampleColour,
        sampling,
        verbose
    )

### Arguments

`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

### Value

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`

### 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)

    annotationDiagnosticPlots(emptyAnnotation)
    # Warning: the object has not been annotated, return an empty diagnostic plot
    # list
    # [[1]]
    # NULL
    # [[2]]
    # NULL
    }

[Package peakPantheR version 1.4.0 Index]