plotNMR: A function for plotting NMR spectra.

In mrbin: Metabolomics Data Analysis Functions

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"),
  density = NULL,
  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,
  ...
)

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
density	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

Value

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

Examples

mrbin(silent=TRUE,setDefault=TRUE,parameters=list(dimension="1D",binwidth1D=.1,
         PQNScaling="No",noiseRemoval="No",trimZeros="No",tryParallel=TRUE,
         fixNegatives="No",logTrafo="No",PCA="No",verbose=TRUE,
         NMRfolders=system.file("extdata/1/10/pdata/10",package="mrbin")))
plotNMR()

mrbin documentation built on April 4, 2025, 5:24 a.m.