plotNMR: A function for plotting NMR spectra.
In mrbin: Metabolomics Data Analysis Functions

plotNMR

R Documentation

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("green", "orange", "blue", "red", "yellow", "gray", "purple"),
  rectangleFront = FALSE,
  polygonRegion = NULL,
  color = NULL,
  add = FALSE,
  showGrid = FALSE,
  manualScale = TRUE,
  plotTitle = "",
  restrictToRange = FALSE,
  currentSpectrumOriginal = NULL,
  perspective = FALSE,
  noise = NULL,
  dimension = NULL,
  plotDelay = 0.1
)

Arguments

`region`	A vector defining the plot region (left, right, top, bottom)
`rectangleRegions`	A 4-column matrix defining areas where to plot rectangles
`rectangleColors`	Define colors 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
`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
`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

Value

None

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 June 22, 2024, 9:39 a.m.