RowDataPlot-class {iSEE}R Documentation

The RowDataPlot panel

Description

The RowDataPlot is a panel class for creating a RowDotPlot where the y-axis represents a variable from the rowData of a SummarizedExperiment object. It provides slots and methods for specifying which variable to use on the y-axis (and, optionally, also the x-axis), as well as a method to create the data.frame in preparation for plotting.

Slot overview

The following slots control the variables to be shown:

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

Constructor

RowDataPlot(...) creates an instance of a RowDataPlot 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 RowDataPlot 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:

For documentation:

Subclass expectations

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

Author(s)

Aaron Lun

See Also

RowDotPlot, for the immediate parent class.

Examples

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

x <- RowDataPlot()
x[["XAxis"]]
x[["XAxis"]] <- "Row data"

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

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

# Spits out a NULL and a warning if is nothing to plot.
sce0 <- .cacheCommonInfo(x, sce)
.refineParameters(x, sce0)

# Replaces the default with something sensible.
rowData(sce)$Stuff <- runif(nrow(sce))
sce0 <- .cacheCommonInfo(x, sce)
.refineParameters(x, sce0)


[Package iSEE version 2.2.4 Index]