AggregatedDotPlot {iSEEu}R Documentation

The AggregatedDotPlot class

Description

Implements an aggregated dot plot where each feature/group combination is represented by a dot. The color of the dot scales with the mean assay value across all samples for a given group, while the size of the dot scales with the proportion of non-zero values across samples in that group.

Slot overview

The following slots control the choice of features:

The following slots control the specification of groups:

The following slots control the choice of assay values:

The following slots control the visualization parameters:

The following slots control the transformation of the mean values:

The following slots control the color:

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

Constructor

AggregatedDotPlot(...) creates an instance of a AggregatedDotPlot 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 an AggregatedDotPlot 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 generating output:

For providing documentation:

Author(s)

Aaron Lun

See Also

Panel, for the immediate parent class.

ComplexHeatmapPlot, for another panel with multi-row visualization capability.

Examples

library(scRNAseq)

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

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

# launch the app itself ----
if (interactive()) {
    iSEE(sce, initial=list(
        AggregatedDotPlot(ColumnDataLabel="Primary.Type")
    ))
}


[Package iSEEu version 1.4.0 Index]