Get or set global values that are used by relevant panels during construction and application initialization.
This has been deprecated in favor of panelDefaults
(for options that apply during Panel construction)
and registerAppOptions
(for options that apply during application runtime).
Commands
str(iSEEOptions$get())
will show the default values for all options.
iSEEOptions$set(name=value)
will set the name
d option to value
.
iSEEOptions$restore()
will reset the global options to the package default values.
Available options
point.color
Default color of data points in
DotPlot
panels (character).point.size
Default size of data points in
DotPlot
panels (numeric).point.alpha
Default alpha level controlling transparency of data points in
DotPlot
panels (numeric).downsample
Enable visual downsampling in
DotPlot
panels (logical).downsample.resolution
Resolution of the visual downsampling, if active (numeric).
selected.color
Color of selected data points in
DotPlot
panels (character).selected.alpha
Alpha level controlling transparency of data points not selected in
DotPlot
panels (numeric).selection.dynamic.single
Toggle dynamic single selections for all panels (logical).
selection.dynamic.multiple
Toggle dynamic multiple selections for all panels (logical).
contour.color
Color of the 2d density estimation contour in
DotPlot
panels (character).font.size
Global multiplier controlling the magnification of plot title and text elements in
DotPlot
panels (numeric).legend.position
Position of the legend in
DotPlot
andComplexHeatmapPlot
panels (one of"Bottom"
,"Right"
).legend.direction
Position of the legend in
DotPlot
andComplexHeatmapPlot
panels (one of"Horizontal"
,"Vertical"
).panel.width
Default panel grid width (must be between 1 and 12).
panel.height
Default panel height (in pixels).
panel.color
Named character vector of colors. The names of the vector should be set to the name of class to be overridden; if a class is not named here, its default color is used. It is highly recommended to define colors as hex color codes (e.g.,
"#1e90ff"
), for full compatibility with both HTML elements and R plots.color.maxlevels
Maximum number of levels for a categorical variable used for coloring. Variables with more levels are coerced to numeric to avoid problems with an overly-large legend. Defaults to 24.
factor.maxlevels
Maximum number of levels for a categorical variable to be used anywhere in the app. Variables with more levels are coerced to numeric to avoid rendering delays. Defaults to 100.
assay
Character vector of assay names to use if available, in order of preference.
RowTable.select.details
A function that takes a string containing the name of a feature (i.e., the current selection in the RowTable) and returns a HTML element with more details.
ColumnTable.select.details
A function that takes a string containing the name of a sample (i.e., the current selection in the ColumnTable) and returns a HTML element with more details.