Additional arguments

Description

Additional arguments that can be passed to rNMR functions.

Details

Many rNMR functions accept additional arguments that get passed to internal plotting and peak picking functions. The option of passing these arguments is provided as a convenience for advanced rNMR users and developers. The various parameters for these functions are described below.

Plotting parameters

add

logical; TRUE adds new data to an existing plot, FALSE generates a new plot.

axes

logical; TRUE makes pretty labels, FALSE puts a box around the plot but no labels.

bg

Background color, see colors for the many color options.

col

Color for 1D data and 1D slices/projections of 2D data. All 2D plots use pos.color for positive intensities, and neg.color for negative intensities. 3D perspective plots use pos.color for all data, and all 1D plots use col.

col.axis

Axis color, see colors for the many color options.

col.lab

Color used for axis labels, see colors for the many color options.

col.main

Color used for plot main titles, see colors for the many color options.

col.sub

Color used for plot sub-titles, see colors for the many color options.

conDisp

logical vector; c(TRUE, TRUE) plots positive and negative contours, c(TRUE, FALSE) plots only positive, c(FALSE, TRUE) plots only the negative contours, c(FALSE, FALSE) plots no contours.

fg

Foreground color, see colors for the many color options.

main

character string; main title for plot, the default is the file name.

neg.color

Color for negative contours, the default is the most recent setting for the file, see colors for the many color options.

neg.zlim

numeric (c(lower, upper)); min and max intensities to be displayed for negative contours, the default is the most recent setting used with the file.

nlevels

positive integer; the number of contour intervals to be drawn, the default is the most recent setting used for the file.

p.window

character string; name of the window (device) to be used, can be "main", "sub", "multi", or "stats".

pos.color

Color for positive contours, the default is the most recent setting for the file, see colors for the many color options.

pos.zlim

numeric (c(lower, upper)); min and max intensities to be displayed for positive contours, the default is the most recent setting used with the file.

type

character string; specifies the type of plot to be generated. 2D data can be drawn as "auto", "image", "contour", "filled", and "persp". Image plots are fastest, contour plots are more detailed, "filled" produces a filled contour plot, "persp" generates a 3D perspective plot, and "auto" (the default) switches between image and contour depending on the amount of data being displayed. 1D plots can also be passed a type. Arguments include "l", "p", and "b" for line, point, and both line and points, respectively. 1D spectra default to "l". 2D data, when passed any of the 1D arguments will invoke proj1D and "l", "p" or "b" will be passed to proj1D. If type is set to NULL, type is taken from the spectrum's last setting.

w1Range

numeric (c(lower, upper)); chemical shift range in the indirect dimension, the default is the most recent setting used with the file.

w2Range

numeric (c(lower, upper)); chemical shift range in the direct dimension, the default is the most recent setting used with the file.

xlab

character string; label for the x-axis, the default is the direct detected nucleus in ppm.

ylab

character string; label for the y-axis, the default is the indirect detected nucleus in ppm.

See plot, image, contour, persp for additional plot parameters and their descriptions.

Peak picking parameters

append

logical; TRUE appends new peaks to the previous peak list.

fancy

logical; FALSE implements a basic peak picker that returns local maxima only (this is fastest), TRUE determines chemical shifts of peaks, groups multiplets, and measures line width.

file.name

character string or vector; name of the file(s) to be peak picked. The default, NULL, will pick the current spectrum. Note: file.name must match one of the values returned when calling names(fileFolder).

internal

logical; TRUE returns the peak list without assigning it to fileFolder, FALSE assigns the list to fileFolder.

noiseFilt

either 0, 1 or 2; 0 does not apply a noise filter, 1 applies a mild filter (adjacent points in the direct dimension must be above the noise threshold), 2 applies a strong filter (all adjacent points must be above the noise threshold.

w1Range

numeric; w1 chemical shift range (c(downfield, upfield)) to be used.

w2Gran

integer; controls granularity of search space, smaller values are more exhaustive, larger values suppress noise.

w2Range

numeric; w2 chemical shift range (c(downfield, upfield)) to be used.

Author(s)

Ian A. Lewis ialewis@nmrfam.wisc.edu, Seth C. Schommer schommer@nmrfam.wisc.edu

See Also

rNMR for other rNMR help topics.