visual-parameters-generics {iSEE} | R Documentation

## Generics for visual DotPlot parameters

### Description

These generics allow subclasses to override the user interface elements controlling visual parameters of DotPlot panels.

### Interface definition

In all of the code snippets below, `x` is a Panel instance and `se` is the SummarizedExperiment object.

- `.defineVisualColorInterface(x, se, select_info)` should return a HTML tag definition that contains UI input elements controlling the `color` aesthetic of `ggplot` objects. Here, `select_info` is a list of two character vectors named `row` and `column`, which specifies the names of panels available for transmitting single selections on the rows/columns respectively. A common use case would involve adding elements to change the default color of the points or to color by a chosen metadata field/assay values.

- `.defineVisualShapeInterface(x, se)` should return a HTML tag definition that contains UI input elements controlling the `shape` aesthetic of `ggplot` objects. A common use case would involve adding elements to change the shape of each point according to a chosen metadata field.

- `.defineVisualSizeInterface(x, se)` should return a HTML tag definition that contains UI input elements controlling the `size` aesthetic of `ggplot` objects. A common use case would involve adding elements to change the size of each point according to a chosen metadata field or assay values.

- `.defineVisualPointInterface(x, se)` should return a HTML tag definition that contains UI input elements controlling other aesthetics of `ggplot` objects. This might include controlling the transparency or downsampling.

- `.defineVisualFacetInterface(x, se)` should return a HTML tag definition that contains UI input elements controlling the `facet_grid` applied to `ggplot` objects. This typically involves providing UI elements to choose the metadata variables to use for faceting.

- `.defineVisualTextInterface(x, se)` should return a HTML tag definition that contains UI input elements controlling the appearance of non-data text elements of `ggplot` objects. This typically involves matters such as the font size and legend position.

- `.defineVisualOtherInterface(x)` should a HTML tag definition that contains UI inputs elements to display in the `"Other"` section of the visual parameters. This is a grab-bag of other parameters that don't fit into the more defined categories above.

A method for any of these generics may also return `NULL`, in which case the corresponding section of the visual parameter box is completely hidden.

All of these generics are called by `.defineInterface` for DotPlot subclasses. Developers of subclasses can simply specialize these generics to change the UI instead of reimplementing `.defineInterface` itself.

When implementing methods for these generics, it is a good idea to make use of information precomputed by `.cacheCommonInfo`. For example, `.cacheCommonInfo,ColumnDotPlot-method` will add vectors specifying whether a variable in the `colData` is valid and discrete or continuous.

### Controlling `ColorBy*Data` choices

`.allowableColorByDataChoices(x, se)` should return a character vector of the allowable row/column data variables to use when `ColorBy` is set to `"Row data"` or `"Column data"` for RowDotPlots and ColumnDotPlots, respectively. The default method will use all available (atomic) variables, but subclasses can specialize this to only allow, e.g., continuous or discrete variables.

### Author(s)

Kevin Rue-Albrecht

[Package iSEE version 2.6.0 Index]