table-generics: Generics for table construction
In csoneson/iSEE: Interactive SummarizedExperiment Explorer

table-generics

R Documentation

Generics for table construction

Description

Generic to control the creation of a data.frame to show in the datatable widget of a Table panel. Table subclasses can specialize methods to modify the behavior of .generateOutput.

Constructing the table

.generateTable(x, envir) generates the data.frame to use in the datatable widget. The following arguments are required:

x, an instance of a Table subclass.
envir, the evaluation environment in which the data.frame is to be constructed. This can be assumed to have se, the SummarizedExperiment object containing the current dataset; possibly col_selected, if a multiple column selection is being transmitted to x; and possibly row_selected, if a multiple row selection is being transmitted to x.

In return, the method should add a tab variable in envir containing the relevant data.frame. This will automatically be passed to the datatable widget as well as being stored in pObjects$contents. The return value should be a character vector of commands that produces tab when evaluated in envir.

Each row of the tab data.frame should correspond to one row or column in the SummarizedExperiment envir$se for RowTables and ColumnTables respectively. Unlike .generateDotPlotData, it is not necessary for all rows or columns to be represented in this data.frame.

Ideally, the number and names of the columns of the data.frame should be fixed for all calls to .generateTable. Violating this principle may result in unpredictable interactions with existing values in the SearchColumns slot. Nonetheless, the app will be robust to mismatches, see filterDT for more details.

Any internal variables that are generated by the commands should be prefixed with . to avoid potential clashes with reserved variable names in the rest of the application.

This generic is called by .generateOutput for Table subclasses. Thus, developers of such subclasses only need to specialize .generateTable to change the table contents, without needing to reimplement the entirety of .generateOutput.

Adding details on the selection

.showSelectionDetails(x) should return a HTML element containing details on the currently selected row, given an instance of a Table subclass x. The identity of the selected row should be extracted from x[["Selected"]]. The element will only be rerendered upon a single selection in the Table. Alternatively, it may return NULL in which case no selection details are shown in the interface.