Skip to contents

Dynamic marker table

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

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))
}