ReducedDimensionPlot-class {iSEE} | R Documentation

## The ReducedDimensionPlot panel

### Description

The ReducedDimensionPlot is a panel class for creating a ColumnDotPlot where the coordinates of each column/sample are taken from the `reducedDims` of a SingleCellExperiment object. It provides slots and methods to specify which dimensionality reduction result to use and to create the data.frame with the coordinates of the specified results for plotting.

### ReducedDimensionPlot slot overview

The following slots control the dimensionality reduction result that is used:

- `Type`, a string specifying the name of the dimensionality reduction result. If `NA`, defaults to the first entry of `reducedDims`.

- `XAxis`, integer scalar specifying the dimension to plot on the x-axis. Defaults to 1.

- `YAxis`, integer scalar specifying the dimension to plot on the y-axis. Defaults to 2.

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

### Constructor

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

For setting up data values:

- `.cacheCommonInfo(x)` adds a `"ReducedDimensionPlot"` entry containing `valid.reducedDim.names`, a character vector of names of valid dimensionality reduction results (i.e., at least one dimension). This will also call the equivalent ColumnDotPlot method.

- `.refineParameters(x, se)` replaces `NA` values in `RedDimType` with the first valid dimensionality reduction result name in `se`. This will also call the equivalent ColumnDotPlot method for further refinements to `x`. If no dimensionality reduction results 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.

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 `"Reduced dimension plot"`.

For creating the plot:

- `.generateDotPlotData(x, envir)` will create a data.frame of reduced dimension coordinates 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.

### Author(s)

Aaron Lun

### See Also

ColumnDotPlot, for the immediate parent class.

### Examples

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

    x <- ReducedDimensionPlot()
    x[["Type"]]
    x[["Type"]] <- "TSNE"

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

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

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

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

[Package iSEE version 2.4.0 Index]