iSEEOptions {iSEE} | R Documentation

## 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 `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` 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')

[Package iSEE version 2.4.0 Index]