metadata-plot-generics {iSEE} | R Documentation

## Generics for row/column metadata plots

### Description

These generics allow subclasses to refine the choices of allowable variables on the x- and y-axes of a ColumnDataPlot or RowDataPlot. This is most useful for restricting the visualization to a subset of variables, e.g., only taking log-fold changes in a y-axis of a MA plot.

### Allowable y-axis choices

`.allowableYAxisChoices(x, se)` takes `x`, a Panel instance; and `se`, the SummarizedExperiment object. It is expected to return a character vector containing the names of acceptable variables to show on the y-axis. For ColumnDataPlots, these should be a subset of the variables in `colData(se)`, while for RowDataPlots, these should be a subset of the variables in `rowData(se)`.

Given a constant `se`, the output of this function should be constant for all instances of the same panel class. As such, 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, which can be intersected with any additional requirements in a subclass's method for this generic.

This generic is called by `.defineDataInterface` for ColumnDataPlots and RowDataPlots. Thus, developers wanting to restrict those choices for subclasses can simply specialize `.allowableYAxisChoices` rather than reimplementing `.defineDataInterface`.

### Allowable x-axis choices

`.allowableXAxisChoices(x, se)` is the same as above but controls the variables that can be shown on the x-axis. This need not return the same subset of variables as `.allowableYAxisChoices`. However, again, the output of this function should be constant for all instances of the same class and a constant `se`.

### Author(s)

Aaron Lun

[Package iSEE version 2.4.0 Index]