AggregatedDotPlot {iSEEu} | R Documentation

## The AggregatedDotPlot class

### Description

Implements an aggregated dot plot where each feature/group combination is represented by a dot. The color of the dot scales with the mean assay value across all samples for a given group, while the size of the dot scales with the proportion of non-zero values across samples in that group.

### Slot overview

The following slots control the choice of features:

- `CustomRows`, a logical scalar indicating whether custom rows in `CustomRowsText` should be used. If `TRUE`, the feature identities are extracted from the `CustomRowsText` slot; otherwise they are defined from a transmitted row selection. Defaults to `TRUE`.

- `CustomRowsText`, a string containing the names of the features of interest, typically corresponding to the row names of the SummarizedExperiment. Names should be new-line separated within this string. Defaults to the name of the first row in the SummarizedExperiment.

The following slots control the specification of groups:

- `ColumnDataLabel`, a string specifying the name of the `colData` field to use to group cells. The chosen field should correspond to a categorical factor. Defaults to the first categorical field.

- `ColumnDataFacet`, a string specifying the name of the `colData` field to use for faceting. The chosen field should correspond to a categorical factor. Defaults to `"---"`, i.e., no faceting.

The following slots control the choice of assay values:

- `Assay`, a string specifying the name of the assay containing continuous values, to use for calculating the mean and the proportion of non-zero values. Defaults to the first valid assay name.

The following slots control the visualization parameters:

- `VisualBoxOpen`, a logical scalar indicating whether the visual parameter box should be open on initialization. Defaults to `FALSE`.

- `VisualChoices`, a character vector specifying the visualization options to show. Defaults to `"Color"` but can also include `"Transform"` and `"Legend"`.

The following slots control the transformation of the mean values:

- `MeanNonZeroes`, a logical scalar indicating whether the mean should only be computed over non-zero values. Defaults to `FALSE`.

- `Center`, a logical scalar indicating whether the means for each feature should be centered across all groups. Defaults to `FALSE`.

- `Scale`, a logical scalar indicating whether the standard deviation for each feature across all groups should be scaled to unity. Defaults to `FALSE`.

The following slots control the color:

- `UseCustomColormap`, a logical scalar indicating whether to use a custom color scale. Defaults to `FALSE`, in which case the application-wide color scale defined by `ExperimentColorMap` is used.

- `CustomColorLow`, a string specifying the low color (i.e., at an average of zero) for a custom scale. Defaults to `"grey"`.

- `CustomColorHigh`, a string specifying the high color for a custom scale. Defaults to `"red"`.

- `CenteredColormap`, a string specifying the divergent colormap to use when `Center` is `TRUE`. Defaults to `"blue < grey < orange"`; other choices are `"purple < black < yellow"`, `"blue < grey < red"` and `"green < grey < red"`.

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

### Constructor

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

For setting up data values:

- `.cacheCommonInfo(x)` adds a `"AggregatedDotPlot"` entry containing `continuous.assay.names` and `discrete.colData.names`.

- `.refineParameters(x, se)` returns `x` after setting `"Assay"`, `"ColumnDataLabel"` and `"ColumnDataFacet"` to valid values. If continuous assays or discrete `colData` variables are not available, `NULL` is returned instead.

For defining the interface:

- `.defineInterface(x, se, select_info)` creates an interface to modify the various parameters in the slots, mostly by calling the parent method and adding another visualization parameter box.

- `.defineDataInterface(x, se, select_info)` creates an interface to modify the data-related parameters, i.e., those that affect the position of the points.

- `.defineOutput(x)` defines the output HTML element.

- `.panelColor(x)` will return the specified default color for this panel class.

- `.fullName(x)` will return `"Aggregated dot plot"`.

- `.hideInterface(x)` will return `TRUE` for UI elements related to multiple row selections.

For monitoring reactive expressions:

- `.createObservers(x, se, input, session, pObjects, rObjects)` will create all relevant observers for the UI elements.

For generating output:

- `.generateOutput(x, se, all_memory, all_contents)` will return the aggregated dot plot as a ggplot object, along with the commands used for its creation.

- `.renderOutput(x, se, output, pObjects, rObjects)` will render the aggregated dot plot onto the interface.

- `.exportOutput(x, se, all_memory, all_contents)` will save the aggregated dot plot to a PDF file named after `x`, returning the path to the new file.

For providing documentation:

- `.definePanelTour(x)` will return a data.frame to be used in rintrojs as a panel-specific tour.

### Author(s)

Aaron Lun

### See Also

Panel, for the immediate parent class.

ComplexHeatmapPlot, for another panel with multi-row visualization capability.

### Examples

    library(scRNAseq)

    # Example data ----
    sce <- ReprocessedAllenData(assays="tophat_counts")
    class(sce)

    library(scater)
    sce <- logNormCounts(sce, exprs_values="tophat_counts")

    # launch the app itself ----
    if (interactive()) {
        iSEE(sce, initial=list(
            AggregatedDotPlot(ColumnDataLabel="Primary.Type")
        ))
    }

[Package iSEEu version 1.4.0 Index]