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

In speaq: Tools for Nuclear Magnetic Resonance (NMR) Spectra Alignment, Peak Based Processing, Quantitative Analysis and Visualizations

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

Author(s)

Charlie Beirnaert, [e-mail]

Examples

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"
                 )

speaq documentation built on May 23, 2022, 5:06 p.m.