ColumnDotPlot-class: The ColumnDotPlot virtual class

In csoneson/SEE: Interactive SummarizedExperiment Explorer

The ColumnDotPlot virtual class

Description

The ColumnDotPlot is a virtual class where each column in the SummarizedExperiment is represented by no more than one point (i.e., a “dot”) in a brushable ggplot plot. It provides slots and methods to extract colData fields to control the per-point aesthetics on the plot. This panel will transmit column identities in both its single and multiple selections, and it can receive multiple column selections but not multiple row selections.

Slot overview

The following slots control coloring of the points:

• ColorByColumnData, a string specifying the colData field for controlling point color, if ColorBy="Column data" (see the Panel class). Defaults to the first valid field (see .cacheCommonInfo below).

• ColorByFeatureNameAssay, a string specifying the assay of the SummarizedExperiment object containing values to use for coloring, if ColorBy="Feature name". Defaults to "logcounts" in getPanelDefault, falling back to the name of the first valid assay (see ?".cacheCommonInfo,DotPlot-method" for the definition of validity).

• ColorBySampleNameColor, a string specifying the color to use for coloring an individual sample on the plot, if ColorBy="Sample name". Defaults to "red" in getPanelDefault.

The following slots control other metadata-related aesthetic aspects of the points:

• ShapeByColumnData, a string specifying the colData field for controlling point shape, if ShapeBy="Column data" (see the Panel class). The specified field should contain categorical values; defaults to the first such valid field.

• SizeByColumnData, a string specifying the colData field for controlling point size, if SizeBy="Column data" (see the Panel class). The specified field should contain continuous values; defaults to the first such valid field.

• TooltipColumnData, a character vector specifying colData fields to show in the tooltip. Defaults to 'character(0)', which displays only the 'colnames' value of the data point.

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

Supported methods

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

For setting up data values:

• .cacheCommonInfo(x) adds a "ColumnDotPlot" entry containing valid.colData.names, a character vector of names of columns that are valid (i.e., contain atomic values); discrete.colData.names, a character vector of names for columns with discrete atomic values; and continuous.colData.names, a character vector of names of columns with continuous atomic values. This will also call the equivalent DotPlot method.

• .refineParameters(x, se) replaces NA values in ColorByFeatAssay with the first valid assay name in se. This will also call the equivalent DotPlot method.

For defining the interface:

• .hideInterface(x, field) returns a logical scalar indicating whether the interface element corresponding to field should be hidden. This returns TRUE for row selection parameters ("RowSelectionSource" and "RowSelectionRestrict"), otherwise it dispatches to the Panel method.

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 DotPlot method.

For controlling selections:

• .multiSelectionRestricted(x) returns a logical scalar indicating whether x is restricting the plotted points to those that were selected in a transmitting panel.

• .multiSelectionDimension(x) returns "column" to indicate that a multiple column selection is being transmitted.

• .multiSelectionInvalidated(x) returns TRUE if the faceting options use multiple column selections, such that the point coordinates/domain may change upon updates to upstream selections in transmitting panels.

• .singleSelectionDimension(x) returns "sample" to indicate that a sample identity is being transmitted.

For documentation:

• .definePanelTour(x) returns an data.frame containing the steps of a tour relevant to subclasses, mostly tuning the more generic descriptions from the same method of the parent DotPlot.

• .getDotPlotColorHelp(x, color_choices) returns a data.frame containing the documentation for the "ColorBy" UI element, specialized for column-based dot plots.

Unless explicitly specialized above, all methods from the parent classes DotPlot and Panel are also available.

Subclass expectations

Subclasses are expected to implement methods for, at least:

• .generateDotPlotData

• .fullName

• .panelColor

The method for .generateDotPlotData should create a plot.data data.frame with one row per column in the SummarizedExperiment object.

Author(s)

Aaron Lun

See Also

DotPlot, for the immediate parent class that contains the actual slot definitions.

csoneson/SEE documentation built on Oct. 13, 2024, 10:19 a.m.