ReducedDimensionHexPlot-class {iSEEu}R Documentation

The ReducedDimensionHexPlot class

Description

The ReducedDimensionHexPlot is a ReducedDimensionPlot subclass that is dedicated to creating a reduced dimension plot summarising data points in hexagonal bins.

Slot overview

The following slots control the parameters used in the visualization:

In addition, this class inherits all slots from its parent ReducedDimensionPlot, ColumnDotPlot, DotPlot and Panel classes.

Constructor

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

For defining the interface:

For monitoring reactive expressions:

For creating the plot:

For documentation:

Author(s)

Kevin Rue-Albrecht

See Also

ReducedDimensionPlot, for the base class.

Examples

library(scRNAseq)

# Example data ----
sce <- ReprocessedAllenData(assays="tophat_counts")
class(sce)

library(scater)
sce <- logNormCounts(sce, exprs_values="tophat_counts")

sce <- runPCA(sce, ncomponents=4)
sce <- runTSNE(sce)
rowData(sce)$ave_count <- rowMeans(assay(sce, "tophat_counts"))
rowData(sce)$n_cells <- rowSums(assay(sce, "tophat_counts") > 0)

# launch the app itself ----

if (interactive()) {
    iSEE(sce, initial=list(
        ReducedDimensionHexPlot(BinResolution=50),
        ReducedDimensionPlot()
    ))
}


[Package iSEEu version 1.5.2 Index]