annotation_diagnostic_multiplot_UI_helper: UI diagnostic plot helper - single feature multiplot

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

UI diagnostic plot helper - single feature multiplot

Description

Return a ggplot object of a feature diagnostic multiplot

Usage

annotation_diagnostic_multiplot_UI_helper(
    cpdNb,
    annotation,
    splNum = NULL,
    splColrColumn = NULL,
    ...
)

Arguments

cpdNb	(int) position of the feature to extract (1 to nbCpd)
annotation	(peakPantheRAnnotation) Annotation object
splNum	(int) NULL or number of spectra to plot, chosen randomly from all spectra. If NULL or equal to the total number of spectra, plot all spectra
splColrColumn	(str) NULL, None or a spectraMetadata column for colouring each sample
...	Additional parameters for plotting

Value

(ggplotObject) Diagnostic multiplot for a feature

Examples

## Initialise a peakPantheRAnnotation object with 3 samples and 2 targeted
## compounds

# Paths to spectra files
spectraPaths <- c('./path/file1', './path/file2', './path/file3')

# 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)

# Plot of an empty annotation
annotation_diagnostic_multiplot_UI_helper(cpdNb = 2,
                                            annotation = emptyAnnotation,
                                            splNum = NULL,
                                            splColrColumn = NULL)
# Warning: the object has not been annotated, return an empty diagnostic
# plot list

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