plotSpecMat: plotSpecMat Overlaid/Stacked Plot

In Rnmr1D: Perform the Complete Processing of a Set of Proton Nuclear Magnetic Resonance Spectra

plotSpecMat Overlaid/Stacked Plot

Description

plotSpecMat Plot spectra set, overlaid or stacked; if stacked, plot with or without a perspective effect.

Usage

plotSpecMat(
  specMat,
  ppm_lim = c(min(specMat$ppm), max(specMat$ppm)),
  K = 0.67,
  pY = 1,
  dppm_max = 0.2 * (max(ppm_lim) - min(ppm_lim)),
  asym = 1,
  beta = 0,
  cols = NULL
)

Arguments

specMat	a 'specMat' object - Spectra matrix in specMat$int (rows = samples, columns = buckets)
ppm_lim	ppm range of the plot
K	Graphical height of the stack (0 .. 1),(default=0.67)
pY	Intensity limit factor (default 1)
dppm_max	Max ppm shift to have a perspective effect
asym	Correction of vertical parallax effect (-1 .. 1) -1 : parallelogram 0 : trapeze with maximum asymmetric 1 : symmetric trapeze
beta	Correction of horizontal parallax effect (0 .. 0.2) (defaut 0)
cols	Vector of colors (same size that the number of spectra, i.e dim(specmat)[1])

Examples

 
  data_dir <- system.file("extra", package = "Rnmr1D")
  cmdfile <- file.path(data_dir, "NP_macro_cmd.txt")
  samplefile <- file.path(data_dir, "Samples.txt")
  out <- Rnmr1D::doProcessing(data_dir, cmdfile=cmdfile, 
                                samplefile=samplefile, ncpu=2)
  # Overlaid plot
  plotSpecMat(out$specMat, ppm_lim=c(0.5,9), K=0, pY=0.1)
  # Stacked plot with perspective effect
  plotSpecMat(out$specMat, ppm_lim=c(-0.1,9),K=0.33)
  # Stacked plot with perspective effect with maximum asymmetric
  plotSpecMat(out$specMat, ppm_lim=c(0.5,5), K=0.33, asym=0)
  cols <- c(rep("red",3), rep("blue",3))
  # Stacked plot with colors accordings to group levels
  plotSpecMat(out$specMat, ppm_lim=c(0.5,5), K=0.67, dppm_max=0, cols=cols)

Rnmr1D documentation built on April 14, 2023, 12:34 a.m.