ColumnDataPlot-class: The ColumnDataPlot panel
In iSEE: Interactive SummarizedExperiment Explorer

Description Slot overview Constructor Supported methods Subclass expectations Author(s) See Also Examples

The ColumnDataPlot is a panel class for creating a ColumnDotPlot where the y-axis represents a variable from the colData 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.

The following slots control the column data information that is used:

YAxis, a string specifying the column of the colData to show on the y-axis. If NA, defaults to the first valid field (see ?".refineParameters,ColumnDotPlot-method").
XAxis, string specifying what should be plotting on the x-axis. This can be any one of "None" or "Column data". Defaults to "None".
XAxisColumnData, string specifying the column of the colData to show on the x-axis. If NA, defaults to the first valid field.

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

ColumnDataPlot(...) creates an instance of a ColumnDataPlot class, where any slot and its value can be passed to ... as a named argument.

In the following code snippets, x is an instance of a ColumnDataPlot class. Refer to the documentation for each method for more details on the remaining arguments.

For setting up data values:

.refineParameters(x, se) returns x after replacing any NA value in YAxis or XAxisColumnData with the name of the first valid colData variable. This will also call the equivalent ColumnDotPlot method for further refinements to x. If no valid column metadata variables are available, NULL is returned instead.

For defining the interface:

.defineDataInterface(x, se, select_info) returns a list of interface elements for manipulating all slots described above.
.panelColor(x) will return the specified default color for this panel class.
.allowableXAxisChoices(x, se) returns a character vector specifying the acceptable variables in colData(se) that can be used as choices for the x-axis. This consists of all variables with atomic values.
.allowableYAxisChoices(x, se) returns a character vector specifying the acceptable variables in colData(se) that can be used as choices for the y-axis. This consists of all variables with atomic values.

For monitoring reactive expressions:

.createObservers(x, se, input, session, pObjects, rObjects) sets up observers for all slots described above and in the parent classes. This will also call the equivalent ColumnDotPlot method.

For defining the panel name:

.fullName(x) will return "Column data plot".

For creating the plot:

.generateDotPlotData(x, envir) will create a data.frame of column metadata variables in envir. It will return the commands required to do so as well as a list of labels.

For documentation:

.definePanelTour(x) returns an data.frame containing a panel-specific tour.

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

Aaron Lun

ColumnDotPlot, for the immediate parent class.

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

x <- ColumnDataPlot()
x[["XAxis"]]
x[["XAxis"]] <- "Column data"

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

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

old_cd <- colData(sce)
colData(sce) <- NULL

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

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