FeatureSetTable-class {iSEEu}R Documentation

Feature set table

Description

A table where each row is itself a feature set and can be clicked to transmit a multiple feature selection to another panel. This relies on feature set collections that have been registered in the input SummarizedExperiment, see registerFeatureSetCollections for more details. If no collections have been registered, we default to the GO and KEGG collections from createGeneSetCommands.

Slot overview

The following slots control the feature sets in use:

The following slots control the table selections:

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

Constructor

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

For setting up data values:

For defining the interface:

For monitoring reactive expressions:

For creating the table:

For controlling the multiple selections:

For documentation:

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"))

cmds <- createGeneSetCommands(collections="GO",
    organism="org.Mm.eg.db", identifier="ENSEMBL")
sce <- registerFeatureSetCommands(sce, cmds)

# Setting up the application.
gst <- FeatureSetTable(PanelId=1L)

rdp <- RowDataPlot(RowSelectionSource="FeatureSetTable1",
    ColorBy="Row selection",
    XAxis="Row data", XAxisRowData="mean", YAxis="total")

rdt <- RowDataTable(RowSelectionSource="FeatureSetTable1")

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


[Package iSEEu version 1.6.0 Index]