setGraphics {rNMR} | R Documentation |
Change graphics settings for one or more open spectra. This function is provided as a convenience for advanced rNMR users and developers.
setGraphics(file.name = currentSpectrum, all.files = FALSE, save.backup = TRUE, refresh.graphics = FALSE, bg = NULL, fg = NULL, col.axis = NULL, col.lab = NULL, col.main = NULL, col.sub = NULL, col = NULL, usr = NULL, line.color = NULL, pos.color = NULL, neg.color = NULL, proj.color = NULL, conDisp = NULL, nlevels = NULL, clevel = NULL, type = NULL, theta = NULL, phi = NULL, asp = NULL, peak.color = NULL, peak.disp = NULL, peak.noiseFilt = NULL, peak.pch = NULL, peak.cex = NULL, peak.labelPos = NULL, thresh.1D = NULL, position.1D = NULL, offset = NULL, proj.mode = NULL, proj.type = NULL, proj.direct = NULL, filter = NULL, roi.multi = NULL, roiMain = NULL, roiMax = NULL, roi.bcolor = NULL, roi.tcolor = NULL, roi.lwd = NULL, roi.lty = NULL, roi.cex = NULL, roi.labelPos = NULL, roi.noiseFilt = NULL, roi.w1 = NULL, roi.w2 = NULL, roi.pad = NULL, w1Range = NULL, w2Range = NULL, overlay.text = NULL)
file.name |
character string or vector; the complete file path(s) to an
open spectrum or spectra to be modified, defaults to the current spectrum.
Note: file.name must match one of the values returned when calling
names(fileFolder) . |
all.files |
logical; if TRUE all files will be updated. |
save.backup |
logical; saves an undo/redo point if TRUE . |
refresh.graphics |
logical; if TRUE all plot windows are
redrawn. |
bg |
see par . |
fg |
see par . |
col.axis |
see par . |
col.lab |
see par . |
col.main |
see par . |
col.sub |
see par . |
col |
see par . |
usr |
see par . |
line.color |
sets the fg , col.axis , col.lab ,
col.main , col.sub , and col parameters to the color
provided (see colors for a list of usable colors). |
pos.color |
color setting for positive contours (see colors
for a list of usable colors). |
neg.color |
color setting for negative contours (see colors
for a list of usable colors). |
proj.color |
color setting for 1D plots and projections (see
colors for a list of usable colors). |
conDisp |
logical vector; c(TRUE, TRUE) plots positive and
negative contours, c(TRUE, FALSE) plots only positive,
c(FALSE, TRUE) plots only negative, c(FALSE, FALSE) plots no
contours. |
nlevels |
positive integer; the number of contour levels. |
clevel |
positive numeric; the number of standard deviations away from the noise that the lowest contour should be drawn. |
type |
specifies the type of plot to be generated; "image " loads
fastest, "contour " produces a contour plot, "filled " produces
a filled contour plot, "persp " produces a 3D perspective plot, and
"auto " chooses the type based on the size of the spectral window.
For 1D spectra, "auto " displays a solid line, "p " displays
only points, and "b " displays points connected by a line. |
theta |
perspective plot control (see persp ). |
phi |
perspective plot control (see persp ). |
asp |
perspective plot control (see persp ). |
peak.color |
color setting for peak markers (see colors
for a list of usable colors). |
peak.disp |
logical; if TRUE peak markers are displayed. |
peak.noiseFilt |
integer; 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) |
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" , or "right" . |
thresh.1D |
numeric; the peak picking threshold for 1D spectra. |
position.1D |
numeric; the vertical position of 1D plots within the spectral window. |
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. |
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. |
proj.direct |
integer 1 or 2 ; if 1 a projection of
the direct dimension is displayed, 2 displays the indirect
dimension. |
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. |
roi.multi |
logical; if TRUE the specified file(s) will appear in
the multiple file window. |
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 2, 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 2, c(active, inactive) . See colors
for a list of usable colors. |
roi.lwd |
numeric vector of length 2; line width for active and inactive
ROI boxes, c(active, inactive) . 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 active and inactive
ROI labels, c(active, inactive) . Equivalent to R's cex
graphical parameter (see par ). |
roi.labelPos |
justification for ROI label text. Must be one of
"top" , "bottom" , "left" , or "right" . |
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. |
w1Range |
numeric vector; chemical shift range (c(lower, upper) )
in the indirect dimension. This is provided as an alternative method for
modifying the usr parameter. |
w2Range |
numeric vector; chemical shift range (c(lower, upper) )
in the direct dimension. This is provided as an alternative method for
modifying the usr parameter. |
overlay.text |
logical; if TRUE the names of overlaid spectrum are
displayed in the plot window. |
Sets graphics parameters for the current spectrum or spectra provided by the
file.name
argument. This includes values found in par
as
well as rNMR specific graphics parameters. Note: All changes are
applied to the files in fileFolder
, with the exception of the
global parameters which are modified in the globalSettings
list.
Ian A. Lewis ialewis@nmrfam.wisc.edu, Seth C. Schommer schommer@nmrfam.wisc.edu
ct
for plot settings; per
for perspective
plot settings; co
for color settings; pj
for 1D
projections and slices; ol
for overlays; pp
for
peak picking; roi
for ROIs; sr
for chemical shift
referencing; toolkit
for other rNMR utility functions.