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Generics for visual DotPlot parameters

Source: R/AllGenerics.R
visual-parameters-generics.Rd

These generics allow subclasses to override the user interface elements controlling visual parameters of DotPlot panels.

Interface definition

In all of the code snippets below, x is a Panel instance and se is the SummarizedExperiment object.

  • .defineVisualColorInterface(x, se, select_info) should return a HTML tag definition that contains UI input elements controlling the color aesthetic of ggplot objects. Here, select_info is a list of two character vectors named row and column, which specifies the names of panels available for transmitting single selections on the rows/columns respectively. A common use case would involve adding elements to change the default color of the points or to color by a chosen metadata field/assay values.

  • .defineVisualShapeInterface(x, se) should return a HTML tag definition that contains UI input elements controlling the shape aesthetic of ggplot objects. A common use case would involve adding elements to change the shape of each point according to a chosen metadata field.

  • .defineVisualSizeInterface(x, se) should return a HTML tag definition that contains UI input elements controlling the size aesthetic of ggplot objects. A common use case would involve adding elements to change the size of each point according to a chosen metadata field or assay values.

  • .defineVisualPointInterface(x, se) should return a HTML tag definition that contains UI input elements controlling other aesthetics of ggplot objects. This might include controlling the transparency or downsampling.

  • .defineVisualFacetInterface(x, se) should return a HTML tag definition that contains UI input elements controlling the facet_grid applied to ggplot objects. This typically involves providing UI elements to choose the metadata variables to use for faceting.

  • .defineVisualTextInterface(x, se) should return a HTML tag definition that contains UI input elements controlling the appearance of non-data text elements of ggplot objects. This typically involves matters such as the font size and legend position.

  • .defineVisualOtherInterface(x) should a HTML tag definition that contains UI inputs elements to display in the "Other" section of the visual parameters. This is a grab-bag of other parameters that don't fit into the more defined categories above.

A method for any of these generics may also return NULL, in which case the corresponding section of the visual parameter box is completely hidden.

All of these generics are called by .defineInterface for DotPlot subclasses. Developers of subclasses can simply specialize these generics to change the UI instead of reimplementing .defineInterface itself.

When implementing methods for these generics, it is a good idea to make use of information precomputed by .cacheCommonInfo. For example, .cacheCommonInfo,ColumnDotPlot-method will add vectors specifying whether a variable in the colData is valid and discrete or continuous.

Controlling ColorBy*Data choices

.allowableColorByDataChoices(x, se) should return a character vector of the allowable row/column data variables to use when ColorBy is set to "Row data" or "Column data" for RowDotPlots and ColumnDotPlots, respectively. The default method will use all available (atomic) variables, but subclasses can specialize this to only allow, e.g., continuous or discrete variables.

Controlling hover choices

.getTooltipUI(x, se, name) should return an HTML tag definition representing information to display in the tooltip that is displayed in DotPlot panels when hovering over a data point. The data point is identified by name, its rownames or colnames value in se.

Author

Kevin Rue-Albrecht