ReducedDimensionPlot-class {iSEE}R Documentation

The ReducedDimensionPlot panel

Description

The ReducedDimensionPlot is a panel class for creating a ColumnDotPlot where the coordinates of each column/sample are taken from the reducedDims of a SingleCellExperiment object. It provides slots and methods for specifying which dimensionality reduction result to use.

ReducedDimensionPlot slot overview

The following slots control the dimensionality reduction result that is used:

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

Constructor

ReducedDimensionPlot(...) creates an instance of a ReducedDimensionPlot 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 ReducedDimensionPlot 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 defining the panel name:

For creating the plot:

Subclasses do not have to provide any methods, as this is a concrete class.

Author(s)

Aaron Lun

See Also

ColumnDotPlot, for the immediate parent class.

Examples

#################
# For end-users #
#################

x <- ReducedDimensionPlot()
x[["Type"]]
x[["Type"]] <- "TSNE"

##################
# For developers #
##################

library(scater)
sce <- mockSCE()
sce <- logNormCounts(sce)

# Spits out a NULL and a warning if no reducedDims are available.
sce0 <- .cacheCommonInfo(x, sce)
.refineParameters(x, sce0)

# Replaces the default with something sensible.
sce <- runPCA(sce)
sce0 <- .cacheCommonInfo(x, sce)
.refineParameters(x, sce0)


[Package iSEE version 2.0.0 Index]