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).

In practice, 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. This can be intersected with additional requirements in this function.

Allowable x-axis choices

.allowableXAxisChoices(x, se) is the same as above but for the variables to show on the x-axis. This need not return the same subset of variables as .allowableYAxisChoices.

Author(s)

Aaron Lun


[Package iSEE version 2.0.0 Index]