options-optionsMRIaggr: Set or Query Default Values for MRIaggr

In bozenne/MRIaggr: Management, Display, and Processing of Medical Imaging Data

Description

optionsMRIaggr works in the same way as options : it can be used to set or query the default values used by the functions of the MRIaggr package.

Usage

optionsMRIaggr(..., reinit.options = FALSE)

Arguments

...	arguments in tag = value form, or a list of tagged values. character or list.
reinit.options	should the default values be reinitialized. logical

Value

If not argument is provided, a list containing all the graphical parameters is returned.
If one argument is provided with no value, the value of the corresponding graphical parameter.
If several arguments are provided, a list containing the corresponding graphical parameters is returned.
If one argument is provided with a value, nothing is returned.

optionsMRIaggr elements

The individual optionsMRIaggr elements are:

asp	the aspect ratio y/x. numeric.
axes	should the axes be plotted ? logical.
bg	the color used for the background. character.
breaks	the break points or the number of breakpoints to use to generate the color intervals . numeric vector or postive integer. Active in multiplot only if argument col is NULL.
cex	the expansion factor used to plot the observations. positive numeric.
cex.index	the expansion factor used to plot each additionnal points to display. integer vector of size 3.
cex.legend	the expansion factor of the legend. positive numeric.
cex.main	the expansion factor for the main title. numeric.
checkArguments	should the validity of thes argments be checked ? logical.
col.index	the color used to plot each additionnal points to display. integer vector of size 3.
col.midplane	the color used to display the midsagittal plan. character.
col.NA	the color to use to plot the NAs. character.
digit.legend	the number of decimal places to use when displaying graphics. integer.
digit.result	the number of decimal places to use when displaying results. integer.
digit.epsilon	the number of decimal places to use when displaying convergence criteria. integer.
digit.percentage	the number of decimal places to use when displaying percentage. integer.
filter.index	the filter used to define the edge of a spatial group. Any of "2D_N4", "2D_N8", "3D_N4", "3D_N6", "3D_N8", "3D_N10", "3D_N18", "3D_N26".
height	the height of the device used to export the plot. postive numeric.
hemisphere	the hemisphere to display. character.
legend	how should the legend be displayed ? logical, NULL or "only".
main	an overall title for the plot. character.
main.legend	a main title for the legend. character.
mar	the number of margin lines to be specified on the four sides of the plot. positive numeric vector of size 4.
mar.legend	the number of margin lines to be specified on the four sides of the legend. numeric vector of size 4.
mfrow	the division of the device in plot region. numeric vector of size 2 or NULL leading automatic adjustment.
mgp	the margin line for the axis title, axis labels and axis line. positive numeric vector of size 3.
norm_mu	the type of centering to apply on the parameter values. character.
norm_sigma	the type of scaling to apply on the parameter values. character.
num.main	should the slice number be written over each plot. logical.
numeric2logical	if a parameter is specified for the index arguments, should it be converted to logical ? logical.
outline.index	should all the additionnal points be displayed or only those on the boundary. logical.
palette	the colors or the palette to use when associating colors to observation intensities. character vector or character. Active in multiplot only if argument col is NULL.
path	the directory where the plot file will be created. character. If path is set to NULL, the image file is exported in the current working directory.
pch.index	the label used to plot each additionnal points to display. integer vector of size 3.
pch.NA	the label to use to plot the NAs. postive integer.
pty	the type of plot region to be used. Can be "s" or "m".
quantiles.legend	should the quantiles of the data be displayed on the legend ? logical.
res	the nominal resolution in ppi which will be recorded in the bitmap file. positive integer.
slice_var	the type of view to use. "i" for sagittal view, "j" for coronal view and "k" for transverse view. character.
type.breaks	should the break points be equally space according the range of data values ("range"), centered ("range_center") or correspond to the quantile values ("quantile") ?
unit	the units in which height and width are given. Can be any of "px", "in", "cm" or "mm"..
verbose	should the execution of the methods related to MRIaggr objects be traced ? logical.
xlab	a title for the x axis. character.
ylab	a title for the y axis. character.
width	the width of the device used to export the plot. postive numeric.
window	the type of device on which the plot will be displayed. logical, NULL or character.

Details

ARGUMENTS:
palette must have be a charater vector of length length(breaks)-1 containing colors or a single character corresponding to a palette name : "rainbow", "grey.colors", "heat.colors", "terrain.colors", "topo.colors" or "cm.colors".

Possible values for legend are:

• TRUE : the legend is displayed in the current device.

• NULL : the legend is displayed it in a new device.

• FALSE : the legend is not displayed.

• "only" : the legend is displayed but not the slices.

Possible values for windows are:

• NULL : the plot is displayed on the current device with no reshape.

• FALSE : the plot is displayed on the current device with the appropriate reshape.

• TRUE : a new graphical device is open.

• "eps" : the plot is displayed in an image file using postscript.

• "svg" : the plot is displayed in an image file using svg.

• "png" : the plot is displayed in an image file using png.

• "pdf" : the plot is displayed in an image file using pdf.

Arguments filename, width, height, path, unit and res correspond to those of postscript, svg and png.

Arguments mfrow, mar, mar.legend, mgp pty, asp and bg acorrespond to those of par.

See the details section of selectContrast for more details about the hemisphere, norm_mu and norm_mu arguments.

See the initNeighborhood function for details about filter.index possible values.

ARGUMENTS:
The MRIaggr environment store an object called .ls_optionsMRIaggr that contains the list of default values. This object can be modified using the optionsMRIaggr function. The original default values can be restored using optionsMRIaggr(reinit.options=TRUE).

Examples

## load a MRIaggr object
data(MRIaggr.Pat1_red, package = "MRIaggr")

# display 3 slices 
multiplot(MRIaggr.Pat1_red, param = "DWI_t0",              
          num = 1:3, axes = FALSE, bg = "white", legend = FALSE)

##
# arguments :
# axes = FALSE, bg = "white", legend = FALSE 
# can become the default argument of multiplot using :
##

optionsMRIaggr(axes = FALSE, bg = "white", legend = FALSE)

multiplot(MRIaggr.Pat1_red, param = "DWI_t0")

# now axes can be restored using either
multiplot(MRIaggr.Pat1_red, param = "DWI_t0", axes = TRUE)
# or
optionsMRIaggr(axes = TRUE)
multiplot(MRIaggr.Pat1_red, param = "DWI_t0")

## to get default arguments of multiplot
optionsMRIaggr()
optionsMRIaggr()$bg
optionsMRIaggr("bg")

## to restore the original defaut values
optionsMRIaggr(reinit.options = TRUE)

bozenne/MRIaggr documentation built on May 13, 2019, 1:39 a.m.