panelDefaults: Panel defaults

In csoneson/iSEE: Interactive SummarizedExperiment Explorer

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 RowDotPlots:

• TooltipRowData, defaults to character(0).

For ColumnDotPlots:

• TooltipColumnData, defaults to character(0).

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")

csoneson/iSEE documentation built on Dec. 13, 2024, 6:14 a.m.