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The FeatureAssayPlot panel

Source: R/panel_FeatureAssayPlot.R
FeatureAssayPlot-class.Rd

The FeatureAssayPlot is a panel class for creating a ColumnDotPlot where the y-axis represents the expression of a feature of interest, using the assay values of the SummarizedExperiment. It provides slots and methods to specify the feature 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:

  • YAxisFeatureName, a string specifying the name of the feature to plot on the y-axis. If NA, defaults to the first row name of the SummarizedExperiment object.

  • Assay, string specifying the name of the assay to use for obtaining expression values. Defaults to "logcounts" in getPanelDefault, falling back to the name of the first valid assay (see ?".cacheCommonInfo,DotPlot-method" for the definition of validity).

  • YAxisFeatureSource, string specifying the encoded name of the transmitting panel to obtain a single selection that replaces YAxisFeatureName. Defaults to "---", i.e., no transmission is performed.

  • YAxisFeatureDynamicSource, a logical scalar indicating whether x should dynamically change its selection source for the y-axis. Defaults to FALSE in getPanelDefault.

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

  • XAxis, string specifying what should be plotting on the x-axis. This can be any one of "None", "Feature name", "Column data" or "Column selection". Defaults to "None".

  • XAxisColumnData, string specifying which column of the colData should be shown on the x-axis, if XAxis="Column data". Defaults to the first valid colData field (see ?".refineParameters,ColumnDotPlot-method" for details).

  • XAaxisFeatureName, string specifying the name of the feature to plot on the x-axis, if XAxis="Feature name". Defaults to the first row name.

  • XAxisFeatureSource, string specifying the encoded name of the transmitting panel to obtain a single selection that replaces XAxisFeatureName. Defaults to "---", i.e., no transmission is performed.

  • XAxisFeatureDynamicSource, a logical scalar indicating whether x should dynamically change its selection source for the x-axis. Defaults to FALSE in getPanelDefault.

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

Constructor

FeatureAssayPlot(...) creates an instance of a FeatureAssayPlot 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 FeatureAssayPlot class. Refer to the documentation for each method for more details on the remaining arguments.

For setting up data values:

  • .refineParameters(x, se) replaces any NA values in XAxisFeatureName and YAxisFeatureName with the first row name; any NA value in Assay with the first valid assay name; and any NA value in XAxisColumnData with the first valid column metadata field. This will also call the equivalent ColumnDotPlot method for further refinements to x. If no rows or assays are present, 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.

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 "Feature assay plot".

For creating the plot:

  • .generateDotPlotData(x, envir) will create a data.frame of feature expression values in envir. It will return the commands required to do so as well as a list of labels.

For managing selections:

  • .singleSelectionSlots(x) will return a list specifying the slots that can be updated by single selections in transmitter panels, mostly related to the choice of feature on the x- and y-axes. This includes the output of the method for the parent ColumnDotPlot class.

  • .multiSelectionInvalidated(x) returns TRUE if the x-axis uses multiple column selections, such that the point coordinates may change upon updates to upstream selections in transmitting panels. Otherwise, it dispatches to the ColumnDotPlot method.

For documentation:

See also

ColumnDotPlot, for the immediate parent class.

Author

Aaron Lun

Examples

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

x <- FeatureAssayPlot()
x[["XAxis"]]
#> [1] "None"
x[["Assay"]] <- "logcounts"
x[["XAxisColumnData"]] <- "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)
#> Panel object of class FeatureAssayPlot
#>   Get or set individual parameters with ‘[[’ 
#>   Available parameters:
#>     Assay: 
#>     BrushData: 
#>     ColorBy: None
#>     ColorByColumnData: Mutation_Status
#>     ColorByDefaultColor: black
#>     ColorByFeatureDynamicSource: FALSE
#>     ColorByFeatureName: Gene_0001
#>     ColorByFeatureNameAssay: 
#>     ColorByFeatureSource: ---
#>     ColorBySampleDynamicSource: FALSE
#>     ColorBySampleName: Cell_001
#>     ColorBySampleNameColor: red
#>     ColorBySampleSource: ---
#>     ColumnSelectionDynamicSource: FALSE
#>     ColumnSelectionRestrict: FALSE
#>     ColumnSelectionSource: ---
#>     ContourAdd: FALSE
#>     ContourColor: blue
#>     CustomLabels: FALSE
#>     CustomLabelsText: Cell_001
#>     DataBoxOpen: FALSE
#>     Downsample: FALSE
#>     DownsampleResolution: 200
#>     FacetColumnBy: None
#>     FacetColumnByColData: Mutation_Status
#>     FacetRowBy: None
#>     FacetRowByColData: Mutation_Status
#>     FixAspectRatio: FALSE
#>     FontSize: 1
#>     HoverInfo: TRUE
#>     LabelCenters: FALSE
#>     LabelCentersBy: Mutation_Status
#>     LabelCentersColor: black
#>     LegendPointSize: 1
#>     LegendPosition: Bottom
#>     PanelHeight: 500
#>     PanelId: NA
#>     PanelWidth: 4
#>     PointAlpha: 1
#>     PointSize: 1
#>     SelectionAlpha: 0.1
#>     SelectionBoxOpen: FALSE
#>     SelectionHistory: 
#>     ShapeBy: None
#>     ShapeByColumnData: Mutation_Status
#>     SizeBy: None
#>     SizeByColumnData: sizeFactor
#>     TooltipColumnData: 
#>     VersionInfo: list of length 1
#>     ViolinAdd: TRUE
#>     VisualBoxOpen: FALSE
#>     VisualChoices: Color
#>     XAxis: None
#>     XAxisColumnData: Mutation_Status
#>     XAxisFeatureDynamicSource: FALSE
#>     XAxisFeatureName: Gene_0001
#>     XAxisFeatureSource: ---
#>     YAxisFeatureDynamicSource: FALSE
#>     YAxisFeatureName: Gene_0001
#>     YAxisFeatureSource: ---
#>     ZoomData: 

# Replaces the default with something sensible.
assayNames(sce) <- old_assay_names
sce0 <- .cacheCommonInfo(x, sce)
.refineParameters(x, sce0)
#> Panel object of class FeatureAssayPlot
#>   Get or set individual parameters with ‘[[’ 
#>   Available parameters:
#>     Assay: logcounts
#>     BrushData: 
#>     ColorBy: None
#>     ColorByColumnData: Mutation_Status
#>     ColorByDefaultColor: black
#>     ColorByFeatureDynamicSource: FALSE
#>     ColorByFeatureName: Gene_0001
#>     ColorByFeatureNameAssay: logcounts
#>     ColorByFeatureSource: ---
#>     ColorBySampleDynamicSource: FALSE
#>     ColorBySampleName: Cell_001
#>     ColorBySampleNameColor: red
#>     ColorBySampleSource: ---
#>     ColumnSelectionDynamicSource: FALSE
#>     ColumnSelectionRestrict: FALSE
#>     ColumnSelectionSource: ---
#>     ContourAdd: FALSE
#>     ContourColor: blue
#>     CustomLabels: FALSE
#>     CustomLabelsText: Cell_001
#>     DataBoxOpen: FALSE
#>     Downsample: FALSE
#>     DownsampleResolution: 200
#>     FacetColumnBy: None
#>     FacetColumnByColData: Mutation_Status
#>     FacetRowBy: None
#>     FacetRowByColData: Mutation_Status
#>     FixAspectRatio: FALSE
#>     FontSize: 1
#>     HoverInfo: TRUE
#>     LabelCenters: FALSE
#>     LabelCentersBy: Mutation_Status
#>     LabelCentersColor: black
#>     LegendPointSize: 1
#>     LegendPosition: Bottom
#>     PanelHeight: 500
#>     PanelId: NA
#>     PanelWidth: 4
#>     PointAlpha: 1
#>     PointSize: 1
#>     SelectionAlpha: 0.1
#>     SelectionBoxOpen: FALSE
#>     SelectionHistory: 
#>     ShapeBy: None
#>     ShapeByColumnData: Mutation_Status
#>     SizeBy: None
#>     SizeByColumnData: sizeFactor
#>     TooltipColumnData: 
#>     VersionInfo: list of length 1
#>     ViolinAdd: TRUE
#>     VisualBoxOpen: FALSE
#>     VisualChoices: Color
#>     XAxis: None
#>     XAxisColumnData: Mutation_Status
#>     XAxisFeatureDynamicSource: FALSE
#>     XAxisFeatureName: Gene_0001
#>     XAxisFeatureSource: ---
#>     YAxisFeatureDynamicSource: FALSE
#>     YAxisFeatureName: Gene_0001
#>     YAxisFeatureSource: ---
#>     ZoomData: