panelDefaults {iSEE} | R Documentation

## Panel defaults

### Description

Get or set default parameters that are used by certain Panel during their construction. This allows users to easily change the defaults for multiple panels simultaneously without having to manually specify them in the constructor.

### Usage

    panelDefaults(...)

    getPanelDefault(name, error = TRUE)

### Arguments

`...` | Named options to set. Alternatively a single named list containing the options to set.
`name` | String containing the name of the option to retrieve. Alternatively `NULL`, in which case the current values of all options are returned as a named list.
`error` | Logical scalar indicating whether an error should be raised if `name` cannot be found.

### Details

All options set by `panelDefaults` will only affect Panel construction and have no effect on the behavior of Panels that are already constructed. Most options are named after the affected slot in the relevant Panel subclass.

For general Panels:

- `PanelWidth`, defaults to 4.

- `PanelHeight`, defaults to 500.

For DotPlots:

- `ColorByDefaultColor`, defaults to `"black"`.

- `PointSize`, defaults to 1.

- `PointAlpha`, defaults to 1.

- `Downsample`, defaults to `FALSE`.

- `DownsampleResolution`, defaults to 200.

- `SelectionAlpha`, defaults to 0.1.

- `ContourColor`, defaults to `"blue"`.

- `FontSize`, defaults to 1.

- `LegendPointSize`, defaults to 1.

For ComplexHeatmapPlots:

- `LegendDirection`, defaults to `"Horizontal"`.

A few options affect multiple subclasses that independently define the same slot:

- `LegendPosition`, defaults to `"Bottom"`. Affects DotPlots and ComplexHeatmapPlots.

- `Assay`, defaults to `"logcounts"`. Affects FeatureAssayPlots, SampleAssayPlots and ComplexHeatmapPlots.

A few options are not named after any particular slot as they affect different slots in different subclasses:

- `ColorByNameColor`, defaults to `"red"`. This affects `ColorByFeatureNameColor` in RowDotPlots and `ColorBySampleNameColor` in ColumnDotPlots.

- `ColorByNameAssay`, defaults to `"logcounts"`. This affects `ColorByFeatureNameAssay` in RowDotPlots and `ColorBySampleNameAssay` in ColumnDotPlots.

- `SingleSelectionDynamicSource`, defaults to `FALSE`. This affects `ColorByFeatureDynamicSource`, `ColorBySampleDynamicSource`, `XAxisFeatureDynamicSource`, `YAxisFeatureDynamicSource`, `XAxisSampleDynamicSource` and `YAxisSampleDynamicSource` in the relevant panels.

- `MultipleSelectionDynamicSource`, defaults to `FALSE`. This affects `RowSelectionDynamicSource` and `ColumnSelectionDynamicSource`.

### Value

`panelDefaults` will return a named list of the values of all options. If `...` is non-empty, `panelDefaults` will modify the global options that are used during the constructors for the relevant Panel classes. (Note that the return value still contains the values before the modification is applied.)

`getPanelDefault` will return the current value of the requested option. If `error=TRUE` and `name` is not present, an error is raised; otherwise `NULL` is returned.

### For developers

Developers of Panel subclasses may add more options to this list, typically by calling `panelDefaults` in the `.onLoad` expressions of the package containing the subclass. We recommend prefixing any options with the name of the package in the form of `<PACKAGE>_<OPTION>`, so as to avoid conflicts with other options (in the base classes, or in other downstream packages) that have the same name. Any options added in this manner should correspond to parameters that are already present as slots in the panel class. If this is not the case, consider using `registerAppOptions` instead.

### Author(s)

Kevin Rue-Albrecht

### Examples

    old <- panelDefaults(Assay="WHEE")
    getPanelDefault("Assay")

    old <- panelDefaults(Assay="FOO", PointSize=5)
    getPanelDefault("Assay")
    getPanelDefault("PointSize")

    # We can also list out all options:
    panelDefaults()

    # Restoring the previous defaults.
    panelDefaults(old)
    getPanelDefault("Assay")
    getPanelDefault("PointSize")

[Package iSEE version 2.4.0 Index]