Default panel options

Description

Set global options using iSEEOptions$set(), so that all relevant panels will use these default values during initialization.

Usage

iSEEOptions

Format

An object of class list of length 4.

Details

See str(iSEEOptions$get()) for a list of default panel options.

Note that iSEEOptions$restore() can be used to 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 and ComplexHeatmapPlot panels (one of "Bottom", "Right").

legend.direction

Position of the legend in DotPlot and ComplexHeatmapPlot 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.

assay

Character vector of assay names to use if available, in order of preference.

Author(s)

Kevin Rue-Albrecht

Examples

iSEEOptions$get('downsample'); iSEEOptions$get('selected.color')