ColumnTable-class: The ColumnTable class

In csoneson/SEE: Interactive SummarizedExperiment Explorer

The ColumnTable class

Description

The ColumnTable is a virtual class where each column in the SummarizedExperiment is represented by no more than row in a datatable widget. In panels of this class, single and multiple selections can only be transmitted on the samples.

Slot overview

No new slots are added. All slots provided in the Table parent class are available.

Supported methods

In the following code snippets, x is an instance of a ColumnTable class. Refer to the documentation for each method for more details on the remaining arguments.

For setting up data values:

• .refineParameters(x, se) replaces NA values in Selected with the first column name of se. This will also call the equivalent Table method.

For defining the interface:

• .hideInterface(x, field) returns a logical scalar indicating whether the interface element corresponding to field should be hidden. This returns TRUE for row selection parameters ("RowSelectionSource" and "RowSelectionRestrict"), otherwise it dispatches to the Panel method.

For monitoring reactive expressions:

• .createObservers(x, se, input, session, pObjects, rObjects) sets up observers to propagate changes in the Selected to linked plots. This will also call the equivalent Table method.

For controlling selections:

• .multiSelectionDimension(x) returns "column" to indicate that a column selection is being transmitted.

• .singleSelectionDimension(x) returns "sample" to indicate that a sample identity is being transmitted.

For rendering output:

• .showSelectionDetails(x) returns a HTML element containing details about the selected row. This requires a function to be registered by registerAppOptions under the option name "ColumnTable.select.details". The function should take a string containing the name of a feature (i.e., the current selection in the ColumnTable) and returns a HTML element. If no function is registered, NULL is returned.

Unless explicitly specialized above, all methods from the parent classes Table and Panel are also available.

Subclass expectations

Subclasses are expected to implement methods for:

• .generateTable

• .fullName

• .panelColor

The method for .generateTable should create a tab data.frame where each row corresponds to a column in the SummarizedExperiment object.

Author(s)

Aaron Lun

See Also

Table, for the immediate parent class that contains the actual slot definitions.

csoneson/SEE documentation built on Oct. 13, 2024, 10:19 a.m.