plotNMR: A function for plotting NMR spectra.

Description

This function plots the current NMR spectrum. If no parameters are provided, parameters are read from the mrbin.env environment variables, set by mrbin. To change the plot, use zoom(), zoomIn(), zoomOut(), intPlus(), intMin(), left(), right(). For 2D data use additionally: contMin(), contPlus(), up(), down()

Usage

plotNMR(
  region = NULL,
  rectangleRegions = NULL,
  rectangleColors = c("darkseagreen3", "orange", "blue", "red", "yellow", "gray",
    "purple"),
  rectangleColors2D = NULL,
  density = NULL,
  angles = 35,
  rectangleFront = FALSE,
  polygonRegion = NULL,
  color = NULL,
  add = FALSE,
  showGrid = FALSE,
  manualScale = TRUE,
  plotTitle = "",
  title = NULL,
  titleCounter = NULL,
  hideNegative = FALSE,
  restrictToRange = FALSE,
  currentSpectrumOriginal = NULL,
  spectrumTMP = NULL,
  renewSpectrum = TRUE,
  cex.axis = 0.7,
  perspective = FALSE,
  noise = NULL,
  dimension = NULL,
  plotDelay = 0.1,
  lwd = 1,
  background = NULL,
  ...
)

Value

An (invisible) dimension-reduced spectrum, either a matrix or a vector

Arguments

region: A vector defining the plot region (left, right, top, bottom) or "all" for the whole spectrum
rectangleRegions: A 4-column matrix defining areas where to plot rectangles
rectangleColors: Define colors for the rectangles
rectangleColors2D: Define colors for rectangles in 2D spectra. If NULL, defaults to the same as rectangleColors
density: Shading lines for the rectangles
angles: Angles of shading lines for the rectangles
rectangleFront: Plot rectangles in front of spectrum rather than in background (only 2D)
polygonRegion: Defines 4 corners of a polygon to be plotted
color: Defines the color of the spectrum plot. If NULL, a rainbow theme is used for 2D NMR
add: If TRUE, additional spectrum plots are overlaid with the current plot
showGrid: Shows a grid of data points. Defaults to FALSE
manualScale: If TRUE, scaling factor is taken from environment variables
plotTitle: Defines the main title of the plot
title: Display the spectrum title in plot, defaults to NULL
titleCounter: Count of the spectrum title for positioning in plot, defaults to NULL
hideNegative: Should negative parts of the 2D spectrum be hidden? Defaults to FALSE
restrictToRange: Restrict plot area to range of available data points. Defaults to FALSE
currentSpectrumOriginal: Optional spectral data. If omitted, data from the environment variables is used
spectrumTMP: A size-reduced spectrum for quicker plotting. Defaults to NULL
renewSpectrum: Should a new size-reduced spectrum for quicker plotting be calculated, or can the old one be used? Default: TRUE
cex.axis: Font size of axis tick labels.
perspective: If TRUE, a perspective plot will be displayed for 2D data instead of the regular topographic view
noise: If provided, a line or plane at this level will be added to the plot to indicate noise level
dimension: "1D' or "2D". If not provided, this will be deduced from the data
plotDelay: Add a small delay in seconds to force RStudio to update plots
lwd: Line width, defaults to 1
background: Background color, defaults to NULL (no background fill, usually results in a white background)
...: Additional graphical parameters that will be passed to the functions plot, lines, and/or contour

Examples

Run this code

resetEnv()#clean up previous data from the package environment 
mrbin(silent=TRUE,setDefault=TRUE,parameters=list(dimension="1D",binwidth1D=.1,
         PQNScaling="No",noiseRemoval="No",trimZeros="No",
         fixNegatives="No",logTrafo="No",PCA="No",verbose=TRUE,NMRvendor="mrbin",
         example=TRUE,#only used for the package examples
         NMRfolders=system.file("extdata/1.mr1",package="mrbin")))
plotNMR()

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