speaq (version 2.7.0)

ROIplot: Plot NMR spectra, together with raw and grouped peaks

Description

This function plots NMR spectra, peak plots and grouped peak plots all in figure for easy comparison.

Usage

ROIplot(
  Y.spec,
  X.ppm,
  ungrouped.peaks,
  grouped.peaks,
  ROI = NULL,
  ROI.ppm = NULL,
  roiWidth = 100,
  roiWidth.ppm = NULL,
  groupLabels = NULL,
  output = NULL
)

Arguments

Y.spec

(required) The raw spectra in matrix format (1 sample per row) or numeric vector (in case of 1 spectrum)

X.ppm

(required) The vector with the ppm values

ungrouped.peaks

(required) The data resulting from peak detection with wavelets

grouped.peaks

(required) The data after grouping (with PeakGrouper)

ROI

If provided (with an index value, not a ppm value) only this region of interest will be plotted. (supply no ROI or ROI.ppm values, for the full spectrum, or specify only 1, either ROI or ROI.ppm).

ROI.ppm

If provided (a ppm value, not an index value) only this region of interest will be plotted. (supply no ROI or ROI.ppm values, for the full spectrum, or specify only 1, either ROI or ROI.ppm).

roiWidth

The width of the ROI (region of interest) plot in index points/measurement points. The plot will span from ROI/ROI.ppm - roiWidth to ROI/ROI.ppm + roiWidth. (only supply roiWidth or roiWidth.ppm if needed).

roiWidth.ppm

The width of the ROI (region of interest) plot in ppm. The plot will span from ROI/ROI.ppm - roiWidth.ppm to ROI/ROI.ppm + roiWidth.ppm. (only supply roiWidth or roiWidth.ppm if needed).

groupLabels

The vector with group labels (as factors)

output

Whether to return a plot (default), or the individual ggplot objects (output = "ggObjects")

Value

a plot

Examples

# NOT RUN {
subset <- GetWinedata.subset()
# to reduce the example time we only select spectra 1 & 2
subset.spectra = as.matrix(subset$Spectra)[1:2,] 
subset.ppm = as.numeric(subset$PPM)

test.peaks <- getWaveletPeaks(Y.spec=subset.spectra, 
                              X.ppm=subset.ppm,
                              nCPU = 1) # nCPU set to 2 for the vignette build

test.grouped <- PeakGrouper(Y.peaks = test.peaks)
                           
ROI.ppm <- 4.9
roiWidth.ppm <- 0.15

plots <- ROIplot(Y.spec = subset.spectra,
                 X.ppm =subset.ppm, 
                 ungrouped.peaks = test.peaks,
                 grouped.peaks = test.grouped ,
                 ROI.ppm = ROI.ppm,
                 roiWidth.ppm = roiWidth.ppm , 
                 output = "ggObjects"
                 )

# }