multi-select-generics: Generics for controlling multiple selections
In iSEE: Interactive SummarizedExperiment Explorer

Description Specifying the dimension Specifying the active selection Evaluating the selection Determining the available points for selection Destroying selections Responding to selections Author(s)

A panel can create a multiple selection on either the rows or columns and transmit this selection to another panel to affect its set of displayed points. For example, users can brush on a DotPlots to select a set of points, and then the panel can transmit the identities of those points to another panel for highlighting.

This suite of generics controls the behavior of these multiple selections. In all of the code chunks shown below, x is assumed to be an instance of the Panel class.

.multiSelectionDimension(x) should return a string specifying whether the selection contains rows ("row"), columns ("column") or if the Panel in x does not perform multiple selections at all ("none"). The output should be constant for all instances of x and is used to govern the interface choices for the selection parameters.

.multiSelectionActive(x) should return some structure containing all parameters required to identify all points in the active multiple selection of x. For example, the DotPlot method for this generic would return the contents of the BrushData slot, usually a list containing a Shiny brush or lasso waypoints for DotPlot classes. If .multiSelectionActive(x) returns NULL, x is assumed to have no active multiple selection.

The active selection is considered to be the one that can be directly changed by the user, as compared to saved selections that are not modifiable (other than being deleted on a first-in-last-out basis). This generic is primarily used to bundle up selection parameters to be stored in the SelectionHistory slot when the user saves the current active selection.

.multiSelectionCommands(x, index) is expected to return a character vector of commands to generate a character vector of row or column names in the desired multiple selection of x. If index=NA, the desired selection is the currently active one; developers can assume that .multiSelectionActive(x) returns a non-NULL value in this case. Otherwise, for an integer index, it refers to the corresponding saved selection in the SelectionHistory.

The commands will be evaluated in an environment containing:

select, a variable of the same type as returned by .multiSelectionActive(x). This will contain the active selection if index=NA and one of the saved selections otherwise. For example, for DotPlots, select will be either a Shiny brush or a lasso structure.
contents, some arbitrary content saved by the rendering expression in .renderOutput(x). This is most often a data.frame but can be anything as long as .multiSelectionCommands knows how to process it. For example, a data.frame of coordinates is stored by DotPlots to identify the points selected by a brush/lasso.
se, the SummarizedExperiment object containing the current dataset.

The output commands are expected to produce a character vector named selected in the evaluation environment. All other variables generated by the commands should be prefixed with . to avoid name clashes.

.multiSelectionAvailable(x, contents) is expected to return an integer scalar specifying the number of points available for selection in the the current instance of the panel x. The contents field in the output of .generateOutput is passed to the contents argument of this generic.

The default method for this generic returns nrow(contents) for all Panel subclasses, assuming that contents is a data.frame where each row represents a point. If not, this method needs to be specialized in order to return an accurate total of available points, which is ultimately used to compute the percentage selected in the multiple selection information panels.

.multiSelectionClear(x) should return x after removing the active selection, i.e., so that nothing is selected. This is used internally to remove multiple selections that do not make sense after protected parameters have changed. For example, a brush or lasso made on a PCA plot in ReducedDimensionPlots would not make sense after switching to t-SNE coordinates, so the application will automatically erase those selections to avoid misleading conclusions.

These generics control how x responds to a transmitted multiple selection, not how x itself transmits selections.

.multiSelectionRestricted(x) should return a logical scalar indicating whether x's displayed contents will be restricted to the selection transmitted from another panel. This is used to determine whether child panels of x need to be re-rendered when x's transmitter changes its multiple selection. For example, in DotPlots, the method for this generic would return TRUE if SelectionEffect="Restrict". Otherwise, it would be FALSE as the transmitted selection is only used for aesthetics, not for changing the identity of the displayed points.

.multiSelectionInvalidated(x) should return a logical scalar indicating whether a transmission of a multiple selection to x invalidates x's own existing selections. This should only be TRUE in special circumstances, e.g., if receipt of a new multiple selection causes recalculation of coordinates in a DotPlot.

Aaron Lun

iSEE documentation built on Feb. 3, 2021, 2:01 a.m.