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.
add
TRUE
adds new data to an existing plot,
FALSE
generates a new plot.axes
TRUE
makes pretty labels, FALSE
puts a box around the plot but no labels.bg
colors
for the many color
options.col
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
colors
for the many color
options.col.lab
colors
for
the many color options.col.main
colors
for the many color options.col.sub
colors
for the many color options.conDisp
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
colors
for the many color
options.main
neg.color
colors
for the many color
options.neg.zlim
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
p.window
main
", "sub
", "multi
", or
"stats
".pos.color
colors
for the many color
options.pos.zlim
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
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
c(lower, upper)
); chemical
shift range in the indirect dimension, the default is the most recent
setting used with the file.w2Range
c(lower, upper)
); chemical
shift range in the direct dimension, the default is the most recent setting
used with the file.xlab
ylab
See plot
, image
, contour
,
persp
for additional plot parameters and their descriptions.
append
TRUE
appends new peaks to the previous
peak list.fancy
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
NULL
, will pick the current spectrum.
Note: file.name
must match one of the values returned when calling
names(fileFolder)
.internal
TRUE
returns the peak list without
assigning it to fileFolder, FALSE
assigns the list to fileFolder.noiseFilt
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
c(downfield, upfield)
) to be used.w2Gran
w2Range
(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.