SampleAssayPlot-class {iSEE}R Documentation

The SampleAssayPlot panel

Description

The SampleAssayPlot is a panel class for creating a RowDotPlot where the y-axis represents the expression of a sample of interest, using the assay values of the SummarizedExperiment. It provides slots and methods for specifying the sample and what to plot on the x-axis, as well as a method to actually create a data.frame containing those pieces of data in preparation for plotting.

Slot overview

The following slots control the values on the y-axis:

The following slots control the values on the x-axis:

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

Constructor

SampleAssayPlot(...) creates an instance of a SampleAssayPlot 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 SampleAssayPlot 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 managing selections:

For documentation:

Author(s)

Aaron Lun

See Also

ColumnDotPlot, for the immediate parent class.

Examples

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

x <- SampleAssayPlot()
x[["XAxis"]]
x[["Assay"]] <- "logcounts"
x[["XAxisRowData"]] <- "stuff"

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

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

old_assay_names <- assayNames(sce)
assayNames(sce) <- character(length(old_assay_names))

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

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


[Package iSEE version 2.5.3 Index]