| addArg {rNMR} | R Documentation |
Additional arguments that can be passed to rNMR functions.
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.
addTRUE adds new data to an existing plot,
FALSE generates a new plot.axesTRUE makes pretty labels, FALSE
puts a box around the plot but no labels.bgcolors for the many color
options.colpos.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.axiscolors for the many color
options.col.labcolors for
the many color options.col.maincolors for the many color options.col.subcolors
for the many color options.conDispc(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.fgcolors for the many color
options.mainneg.colorcolors for the many color
options.neg.zlimc(lower, upper)); min and max
intensities to be displayed for negative contours, the default is the most
recent setting used with the file.nlevelsp.windowmain", "sub", "multi", or
"stats".pos.colorcolors for the many color
options.pos.zlimc(lower, upper)); min and
max intensities to be displayed for positive contours, the default is the
most recent setting used with the file.typeauto", "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.w1Rangec(lower, upper)); chemical
shift range in the indirect dimension, the default is the most recent
setting used with the file.w2Rangec(lower, upper)); chemical
shift range in the direct dimension, the default is the most recent setting
used with the file.xlabylab
See plot, image, contour,
persp for additional plot parameters and their descriptions.
appendTRUE appends new peaks to the previous
peak list.fancyFALSE 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.nameNULL, will pick the current spectrum.
Note: file.name must match one of the values returned when calling
names(fileFolder).internalTRUE returns the peak list without
assigning it to fileFolder, FALSE assigns the list to fileFolder.noiseFilt0, 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.w1Rangec(downfield, upfield)) to be used.w2Granw2Range(c(downfield, upfield)) to be used.Ian A. Lewis ialewis@nmrfam.wisc.edu, Seth C. Schommer schommer@nmrfam.wisc.edu
rNMR for other rNMR help topics.