drawSpecPPM: Plot NMR spectra from a spectra data matrix

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

Plot NMR spectra from a spectra data matrix

Description

This function plots NMR spectra (so with the largest ppm values on the left) with a number of plotting options

Usage

drawSpecPPM(
  Y.spec,
  X.ppm,
  LeftIndex = -1,
  RightIndex = -1,
  groupFactor = NULL,
  useLog = FALSE,
  maxHeight = -1,
  minHeight = -1,
  nAxisPos = 4,
  xlab = NULL,
  ylab = NULL,
  title = NULL,
  ticks = NULL,
  ROI = NULL,
  ROI.ppm = NULL,
  roiWidth = 100,
  roiWidth.ppm = NULL,
  legend.extra.x = 2,
  legend.extra.y = 2,
  legendpos = NULL,
  colourstyle = "ggplot",
  manual.colours = NULL,
  lwd = 1,
  noLegend = FALSE
)

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
LeftIndex	The starting index of the ppm values for plotting. default = -1 indicates the first ppm (the largest) value is the start of the plot
RightIndex	The stopping index for plotting. default = -1 indicates the last ppm value (the smallest) is the end of the plot
groupFactor	The groupFactors. If provided different colors will be used for each group.
useLog	If set to 'TRUE' the spectra will be log10 transformed (default = FALSE).
maxHeight	The maximal height of the plot (default = -1, this indicates no maximal value).
minHeight	The minimal height of the plot (default = -1, this indicates no minimal value).
nAxisPos	The number of equally spaced tickmarks.
xlab	The label on the x axis.
ylab	The label on the y axis.
title	The title of the plot.
ticks	Position tick manually by providing ppm values.
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).
legend.extra.x	Increase (or decrease) the horizontal space in the legend, this is useful for exporting larger figures.
legend.extra.y	Increase (or decrease) the vertical space in the legend, this is useful for exporting larger figures.
legendpos	The position of the legend (standard R legend positioning, default = 'topleft').
colourstyle	The colours used in the plot, either standard R or ggplot colours (default).
manual.colours	Provide specific colours to be used in the plot.
lwd	The linewidth.
noLegend	If set to TRUE no legend will be plotted (default = FALSE).

Value

an R plot

Author(s)

Charlie Beirnaert, [e-mail]

Examples

data(Winedata)
Spectra = Winedata$spectra 
ppm.wine = Winedata$ppm
wine.color = Winedata$wine.color 
drawSpecPPM(Y.spec=Spectra, X.ppm=ppm.wine, groupFactor = wine.color, 
title = 'Raw wine data spectra')

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