ReducedDimensionHexPlot-class {iSEEu} | R Documentation

## The ReducedDimensionHexPlot class

### Description

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

### Slot overview

The following slots control the parameters used in the visualization:

- `BinResolution`, a numeric positive scalar specifying the number of hexagonal bins in both vertical and horizontal directions. Defaults to 100.

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:

- `.panelColor(x)` will return the specified default color for this panel class.

- `.hideInterface(x, field)` will return `TRUE` for `field="Downsample"`, otherwise it will call the ReducedDimensionPlot method.

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 ReducedDimensionPlot method.

For defining the panel name:

- `.fullName(x)` will return `"Hexagonal reduced dimension plot"`.

### 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 1.0.1 Index]