iSEEOptions: Global 'iSEE' options

In csoneson/SEE: Interactive SummarizedExperiment Explorer

Global iSEE options

Description

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).

Usage

iSEEOptions

Format

An object of class list of length 4.

Commands

str(iSEEOptions$get()) will show the default values for all options.

iSEEOptions$set(name=value) will set the named 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 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.

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.

Author(s)

Kevin Rue-Albrecht

Examples

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

csoneson/SEE documentation built on Oct. 13, 2024, 10:19 a.m.