DifferentialStatisticsTable-class {iSEEu}R Documentation

Differential statistics table

Description

A table that dynamically computes differential statistics based on 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 thresholds used in the visualization:

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

Constructor

DifferentialStatisticsTable(...) creates an instance of a DifferentialStatisticsTable 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 setting up data values:

For defining the interface:

For monitoring reactive expressions:

For creating the table:

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

rdp <- ReducedDimensionPlot(PanelId=1L,
    ColorByFeatureSource="DifferentialStatisticsTable1")

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


[Package iSEEu version 1.0.1 Index]