GeneSetTable-class {iSEEu} | R Documentation

## Gene set table

### Description

A table where each row is a gene set and can be clicked to transmit a multiple feature selection to another panel. This usually requires some set-up with `.setIdentifierType` and related functions, see Examples.

### Slot overview

The following slots control the thresholds used in the visualization:

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

- `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 DifferentialStatisticsTable 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.

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.

- `.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(s)

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")
    .setIdentifierType("ENSEMBL")
    gst <- GeneSetTable(PanelId=1L)

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

    rdt <- RowDataTable(RowSelectionSource="GeneSetTable1")

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

[Package iSEEu version 1.0.1 Index]