R: Change graphics settings

setGraphics {rNMR}

R Documentation

Change graphics settings

Description

Change graphics settings for one or more open spectra. This function is provided as a convenience for advanced rNMR users and developers.

Usage

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)

Arguments

`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.

Details

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.

Author(s)