plotUtils {rNMR} | R Documentation |
Utilities for plotting one and two-dimensional spectra in rNMR.
draw2D(in.folder = fileFolder[[wc()]], w1Range = in.folder$graphics.par$usr[3:4], w2Range = in.folder$graphics.par$usr[1:2], pos.zlim = c(in.folder$file.par$noise_est * in.folder$graphics.par$clevel, in.folder$file.par$noise_est * in.folder$graphics.par$clevel * in.folder$graphics.par$nlevels), neg.zlim = -(rev(pos.zlim)), type = in.folder$graphics.par$type, pos.color = in.folder$graphics.par$pos.color, neg.color = in.folder$graphics.par$neg.color, nlevels = in.folder$graphics.par$nlevels, conDisp = in.folder$graphics.par$conDisp, xlab = paste(in.folder$file.par$nucleus[2], "PPM", sep = " "), ylab = paste(in.folder$file.par$nucleus[1], "PPM", sep = " "), main = in.folder$file.par$user_title, roiMax = globalSettings$roiMax, add = FALSE, axes = TRUE, ...) drawNMR(in.folder = fileFolder[[wc()]], w1Range, w2Range, pos.zlim, neg.zlim, type, pos.color, neg.color, nlevels, conDisp, bg, fg, col.axis, col.lab, col.main, col.sub, col, xlab = NULL, ylab = NULL, main = in.folder$file.par$user_title, add = FALSE, p.window = "main", axes = TRUE, offset = 0, ...) plot1D(in.folder = fileFolder[[wc()]], w1Range = in.folder$graphics.par$usr[3:4], w2Range = in.folder$graphics.par$usr[1:2], col = in.folder$graphics.par$proj.color, type = in.folder$graphics.par$type, xlab = NULL, ylab = NULL, main = in.folder$file.par$user_title, roiMax = globalSettings$roiMax, add = FALSE, axes = TRUE, offset = 0, ...) plot2D(in.folder = fileFolder[[wc()]], w1Range = in.folder$graphics.par$usr[3:4], w2Range = in.folder$graphics.par$usr[1:2], pos.zlim = c(in.folder$file.par$noise_est * in.folder$graphics.par$clevel, in.folder$file.par$noise_est * in.folder$graphics.par$clevel * in.folder$graphics.par$nlevels), neg.zlim = -(rev(pos.zlim)), type = in.folder$graphics.par$type, pos.color = in.folder$graphics.par$pos.color, neg.color = in.folder$graphics.par$neg.color, nlevels = in.folder$graphics.par$nlevels, conDisp = in.folder$graphics.par$conDisp, xlab = paste(in.folder$file.par$nucleus[2]), ylab = paste(in.folder$file.par$nucleus[1]), main = in.folder$file.par$user_title, add = FALSE, axes = TRUE, ...) proj1D(in.folder = fileFolder[[wc()]], w1Range = in.folder$graphics.par$usr[3:4], w2Range = in.folder$graphics.par$usr[1:2], col = in.folder$graphics.par$proj.color, filter = globalSettings$filter, proj.direct = globalSettings$proj.direct, type = globalSettings$proj.type, xy = NULL, ...) ucsf1D(file.name = NULL, w2Range = NULL, file.par = NULL) ucsf2D(file.name = NULL, w1Range = NULL, w2Range = NULL, file.par = NULL) ucsfHead(file.name = NULL, print.info = TRUE)
in.folder |
list; file and graphics parameters for the file to be plotted
as listed in fileFolder . |
w1Range |
numeric vector; chemical shift range in the indirect dimension,
default is the most recent setting used with the file, the format is
c(lower,upper) . |
w2Range |
numeric vector; chemical shift range in the direct dimension,
default is the most recent setting used with the file. The format is
c(lower,upper) . |
pos.zlim |
numeric vector; min and max positive intensities to be
displayed, default is the most recent setting used with the file. The
format is c(lower,upper) . |
neg.zlim |
numeric vector; min and max negative intensities to be
displayed, default is the most recent setting used with the file. The
format is c(lower,upper) . |
type |
see plot . |
pos.color |
character string; color for positive contours, default is the
most recent setting for the file, see colors for the many
color options. |
neg.color |
character string; color for negative contours, default is the
most recent setting for the file, see colors for the many
color options. |
nlevels |
numeric; the number of contour intervals to be drawn, the default is the most recent setting used for the file. |
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) does not plot any contours. |
xlab |
see plot . |
ylab |
see plot . |
main |
see plot . |
roiMax |
logical; if TRUE , plots a point on the maximum visible
signal in the window. |
add |
logical; if TRUE , adds new data to an existing plot,
if FALSE generates a new plot. |
axes |
logical; if TRUE , makes pretty labels. |
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 . |
p.window |
character string; the window to be used for the plot, can be
"main" , "sub" , "multi" , or "stats" . |
offset |
numeric; the percentage of the total z range with which to displace a spectrum. This is used to create stacked 1D spectra. |
filter |
function; a vector capable function (e.g. min, max, sd) used to filter 2D data into a 1D projection, non function arguments prompt users to select a slice. |
proj.direct |
numeric; 1 projects data across the direct axis,
2 across the indirect. |
xy |
numeric; x and y coordinates indicating the slice to display. The optional argument may be supplied as an alternative to interactive slice selection. |
file.name |
character string; full path for the file to be read,
NULL will open a file selection window. |
file.par |
list; file parameters as found in the header of the ucsf file
designated by the file.name parameter. This argument is optional and
is used to speed up graphics by foregoing noise estimation. |
... |
additional graphics parameters can be passed to par . |
print.info |
logical; prints header information if TRUE . |
draw2D
plot2D
when creating ROI subplot and multiple file
windows, as it is more efficient for batch operations.drawNMR
plot1D
and plot2D
proj1D
ucsf1D
and ucsf2D
ucsfHead
fileFolder
.
ucsf1D()
and ucsf2D()
return a list containing:
file.par
- Header information for the spectrum including file name,
nuclei, number of dimensions, spectrum width, etc.
w1
- Chemical shifts in the indirect dimension.
w2
- Chemical shifts in the direct dimension.
data
- The data from the spectrum, as a matrix of intensities for 2D
spectra or a vector for 1D slices and plots. The first data point in a
matrix of 2D intensities, [1, 1], corresponds to the downfield-most point,
in both dimensions, for the spectrum. The last data point in the matrix
corresponds to the upfield-most point, in both dimensions, for the spectrum.
In other words, if you traverse the matrix by rows, data points in the
matrix start at the bottom-left of the spectrum and move up and to the right
(as the spectrum would normally be viewed). See import
for
details on the contents of the ROI table, ROI summary, and peak list
objects.
ucsfHead()
returns a list containing the same fields present in the
"file.par" section of fileFolder
.
Ian A. Lewis ialewis@nmrfam.wisc.edu, Seth C. Schommer schommer@nmrfam.wisc.edu
toolkit
for other rNMR utility functions.