annotation_diagnostic_multiplot_UI_helper {peakPantheR} | R Documentation |
Return a ggplot object of a feature diagnostic multiplot
annotation_diagnostic_multiplot_UI_helper( cpdNb, annotation, splNum = NULL, splColrColumn = NULL, ... )
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 |
(ggplotObject) Diagnostic multiplot for a feature
## 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