Description Usage Arguments Value optionsMRIaggr elements Details Examples
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.
1 | optionsMRIaggr(..., reinit.options = FALSE)
|
... |
arguments in tag = value form, or a list of tagged values. character or list. |
reinit.options |
should the default values be reinitialized. logical |
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.
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. |
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)
.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 | ## 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)
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