globalSettings {rNMR} | R Documentation |
The globalSettings
object stores the current set of global graphics and
plot settings as a named list (detailed below). The values for these parameters
are taken from defaultSettings
when rNMR loads.
offset |
numeric; the percent of total intensity range with which to displace each spectrum. This is used to create stacked 1D spectra and is not passed to 2D plots. |
position.1D |
numeric; the vertical position of 1D plots within the spectral window. |
filter |
function; a function used to create a 1D projection, must be
capable of being applied to a vector (e.g. min , max ,
sd ). Function must accept x as its only argument. |
proj.direct |
integer 1 or 2 ; if 1 a projection of
the direct dimension is displayed, 2 displays the indirect
dimension. |
proj.mode |
logical; if TRUE displays a 1D representation of a
2D spectrum. |
proj.type |
specifies the type of projection to be generated;
"auto " displays a solid line, "p " displays only points, and
"b " displays points connected by a line. |
peak.disp |
logical; if TRUE markers and labels are displayed over
picked peaks. |
peak.noiseFilt |
integer; peak picking filter. 0 does not apply a
noise filter, 1 applies a mild filter (adjacent points in the direct
dimension must be above the noise threshold), and 2 applies a strong
filter (all adjacent points must be above the noise threshold). |
thresh.1D |
numeric; the peak picking threshold for 1D spectra. |
peak.pch |
integer or character; the symbol used for peak markers for
picked peaks. Equivalent to R's pch graphical parameter, accepts any
ASCII character as well as integer values corresponding to predefined
symbols in R (see par ). |
peak.cex |
numeric (positive); the magnification for peak labels and
markers for picked peaks. Equivalent to R's cex graphical parameter
(see par ). |
peak.labelPos |
justification for peak label text. Must be one of
"top" , "bottom" , "left" , "right" , or
"center" . |
roiMain |
logical; if TRUE displays ROIs in the main plot
window. |
roiMax |
logical; if TRUE displays a marker in the subplot and
multiple file windows on the absolute maximum visible signals within the
ROIs. |
roi.bcolor |
color setting for active and inactive ROI boxes. Must be
a vector of length two: c(active, inactive) . See colors
for a list of usable colors. |
roi.tcolor |
color setting for active and inactive ROI labels. Must be
a vector of length two: c(active, inactive) . See colors
for a list of usable colors. |
roi.lwd |
numeric; line width for ROI boxes. Equivalent to R's
lwd graphical parameter (see par ). |
roi.lty |
box type for active and inactive ROIs. Must be a vector of
length 2, c(active, inactive) . Equivalent to R's lty
graphical parameter (see par ). Valid options include:
"solid" , "dashed" , "dotted" , "dotdash" ,
"longdash" , "twodash" , or "blank" . |
roi.cex |
numeric (positive); text magnification for ROI labels.
Equivalent to R's cex graphical parameter (see par ). |
roi.labelPos |
justification for ROI label text. Must be one of
"top" , "bottom" , "left" , "right" , or
"center" . |
roi.noiseFilt |
integer; filter for automatic ROI generation (see
ra ). 0 does not apply a noise filter, 1 applies
a mild filter (adjacent points in the direct dimension must be above the
noise threshold), and 2 applies a strong filter (all adjacent points
must be above the noise threshold). Note that setting the ROI noise filter
to zero may result in errors when using ra in certain
spectra. |
roi.w1 |
numeric; fixed size in the indirect dimension (in ppm) for ROIs
generated automatically using ra . |
roi.w2 |
numeric; fixed size in the direct dimension (in ppm) for ROIs
generated automatically using ra . |
roi.pad |
numeric; padding percentage applied to ROIs generated
automatically using ra . This padding is added to the area
surrounding the peaks within an ROI and is only applied to the height/width
of an ROI if the corresponding roi.w1 /roi.w2 argument is not
provided.
|
cex.roi.multi |
numeric (positive); the magnification for ROI labels in
the multiple file window (see rvm ). Equivalent to R's
cex graphical parameter (see par ). |
cex.files.multi |
numeric (positive); the magnification for file names
in the multiple file window (see rvm ). Equivalent to R's
cex graphical parameter (see par ). |
cex.roi.sub |
numeric (positive); the magnification for ROI labels in the
subplot window (see rvs ). Equivalent to R's cex
graphical parameter (see par ). |
size.main |
numeric; the dimensions (in inches) for the main plot
window, of the form c(width, height) . |
size.sub |
numeric; the dimensions (in inches) for the subplot window, of
the form c(width, height) . |
size.multi |
numeric; the dimensions (in inches) for the multiple file
window, of the form c(width, height) . |
mar |
numeric; the number of lines of margin space to be used in the main
plot window. See par . |
mar.sub |
numeric; the number of lines of margin space to be used in the
subplot window (in between ROI plots). Equivalent to R's mar
graphical parameter (see par ). |
mar.multi |
numeric; the number of lines of margin space to be used in
the multiple file window (in between ROI plots). Equivalent to R's
mar graphical parameter (see par ). |
Ian A. Lewis ialewis@nmrfam.wisc.edu, Seth C. Schommer schommer@nmrfam.wisc.edu
rNMRobjects
for other other objects used by the
rNMR package; rNMRutils
for functions used for interacting
with rNMR objects.