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Gene set table

Source: R/GeneSetTable.R
GeneSetTable-class.Rd

A table where each row is a gene set and can be clicked to transmit a multiple feature selection to another panel. This has been deprecated in favor of the simpler FeatureSetTable.

Slot overview

The following slots control the type of gene sets to show:

  • Type, string specifying the type of gene set collection to show. Defaults to "GO".

The following slots control the table selections:

  • Selected, a string containing the name of the currently selected gene set. Defaults to "", i.e., no selection.

  • Search, a string containing the regular expression for the global search. Defaults to "", i.e., no search.

  • SearchColumns, a character vector where each entry contains the search string for each column. Defaults to an empty character vector, i.e., no search.

In addition, this class inherits all slots from its parent Panel class.

Constructor

GeneSetTable(...) creates an instance of a GeneSetTable class, where any slot and its value can be passed to ... as a named argument.

Supported methods

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

For defining the interface:

  • .defineDataInterface(x, se, select_info) returns a list of interface elements for manipulating all slots described above.

  • .panelColor(x) will return the specified default color for this panel class.

  • .fullName(x) will return "Gene set table".

  • .hideInterface(x) will return TRUE for UI elements related to multiple selections, otherwise calling the method for Panel.

  • .defineOutput(x) will return a HTML element containing a datatable widget.

For monitoring reactive expressions:

  • .createObservers(x, se, input, session, pObjects, rObjects) sets up observers for all new slots described above, as well as in the parent classes via the Panel method.

For creating the table:

  • .generateOutput(x, envir) will create a data.frame of gene set descriptions in envir, based on the mode="show" output of .getGeneSetCommands. It will also return the commands required to do so and the name of the variable corresponding to said data.frame.

  • .renderOutput(x, se, ..., output, pObjects, rObjects) will add a datatable widget to the output, which is used to render the aforementioned data.frame.

For controlling the multiple selections:

  • .multiSelectionDimension(x) returns "row".

  • .multiSelectionCommands(x, index) returns a string specifying the commands to be used to extract the identities of the genes in the currently selected set, based on the mode="extract" output of .getGeneSetCommands. index is ignored.

  • .multiSelectionActive(x) returns the name of the currently selected gene set, unless no selection is made, in which case NULL is returned.

  • .multiSelectionClear(x) returns x but with the Selected slot replaced by an empty string.

  • .multiSelectionAvailable(x, contents) returns contents$available, which is set to the number of features in se.

Author

Aaron Lun

Examples

library(scRNAseq)
sce <- LunSpikeInData(location=FALSE)

library(scater)
sce <- logNormCounts(sce)

library(scran)
rowData(sce) <- cbind(rowData(sce), modelGeneVarWithSpikes(sce, "ERCC"))

# This defaults to 'org.Hs.eg.db' with 'ENTREZID'.
.setOrganism("org.Mm.eg.db")
#> Warning: '.setOrganism' is deprecated.
#> Use 'setFeatureSetCommands' instead.
#> See help("Deprecated")
.setIdentifierType("ENSEMBL")
#> Warning: '.setIdentifierType' is deprecated.
#> Use 'setFeatureSetCommands' instead.
#> See help("Deprecated")
gst <- GeneSetTable(PanelId=1L)
#> Warning: 'GeneSetTable' is deprecated.
#> Use 'FeatureSetTable' instead.
#> See help("Deprecated")

rdp <- RowDataPlot(RowSelectionSource="GeneSetTable1",
    ColorBy="Row selection",
    XAxis="Row data", XAxisRowData="mean", YAxis="total")

rdt <- RowDataTable(RowSelectionSource="GeneSetTable1")

if (interactive()) {
    iSEE(sce, initial=list(gst, rdp, rdt))
}