DynamicMarkerTable-class {iSEEu} | R Documentation

## Dynamic marker table

### Description

A table that dynamically identifies marker genes for a selected subset of samples. Comparisons are made between the active selection in the transmitting panel and (i) all non-selected points, if no saved selections are available; or (ii) each subset of points in each saved selection.

### Slot overview

The following slots control the test procedure:

- `LogFC`, a numeric scalar indicating the log-fold change threshold to test against. Defaults to zero.

- `TestMethod`, string indicating the test to use (based on the `findMarkers` function from scran). This can be `"t"` (default), `"wilcox"` or `"binom"`.

- `Assay`, string indicating the assay to use for testing. Defaults to the first named assay in the SummarizedExperiment.

The following slots control the rendered table:

- `ExtraFields`, a character vector containing names of `rowData` columns to be included in the table. Set to the output of `getTableExtraFields`. This cannot be changed once the application starts.

In addition, this class inherits all slots from its parent RowTable, Table and Panel classes.

### Constructor

`DynamicMarkerTable(...)` creates an instance of a DynamicMarkerTable 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 DynamicMarkerTable class. Refer to the documentation for each method for more details on the remaining arguments.

For setting up data values:

- `.cacheCommonInfo(x)` adds a `"DynamicMarkerTable"` entry containing `valid.assay.names` and `valid.rowdata.names`. This will also call the equivalent RowTable method.

- `.refineParameters(x, se)` returns `x` after setting `"Assay"` to the first valid value. This will also call the equivalent RowTable method for further refinements to `x`. If valid assay names are not available, `NULL` is returned instead. Any `"ExtraFields"` are intersected with the valid `rowData` names.

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 `"Dynamic marker table"`.

- `.hideInterface(x)` will return `TRUE` for UI elements related to multiple row selections, otherwise calling the method for RowTable.

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 RowTable method.

For creating the table:

- `.generateTable(x, envir)` will create a data.frame of newly computed statistics in `envir`. The method will return the commands required to do so.

For documentation:

- `.definePanelTour(x)` returns an data.frame containing the steps of a panel-specific tour.

### Examples

    library(scRNAseq)
    library(scater)

    sce <- ReprocessedAllenData(assays="tophat_counts")
    sce <- logNormCounts(sce, exprs_values="tophat_counts")
    sce <- runPCA(sce, ncomponents=4)
    sce <- runTSNE(sce)

    dst <- DynamicMarkerTable(PanelId=1L, PanelWidth=8L,
        ColumnSelectionSource="ReducedDimensionPlot1")

    rdp <- ReducedDimensionPlot(PanelId=1L,
        ColorByFeatureSource="DynamicMarkerTable1")

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

[Package iSEEu version 1.2.0 Index]