ColumnDataTable-class {iSEE} | R Documentation

## The ColumnDataTable panel

### Description

The ColumnDataTable is a panel class for creating a ColumnTable where the value of the table is defined as the `colData` of the SummarizedExperiment. It provides functionality to extract the `colData` to coerce it into an appropriate data.frame in preparation for rendering.

### Slot overview

This class inherits all slots from its parent ColumnTable and Table classes.

### Constructor

`ColumnDataTable(...)` creates an instance of a ColumnDataTable class, where any slot and its value can be passed to `...` as a named argument.

Note that `ColSearch` should be a character vector of length equal to the total number of columns in the `colData`, though only the entries for the atomic fields will actually be used.

### Supported methods

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

For setting up data values:

- `.cacheCommonInfo(x)` adds a `"ColumnDataTable"` entry containing `valid.colData.names`, a character vector of names of atomic columns of the `colData`. This will also call the equivalent ColumnTable method.

- `.refineParameters(x, se)` adjusts `ColSearch` to a character vector of length equal to the number of atomic fields in the `colData`. This will also call the equivalent ColumnTable method for further refinements to `x`.

For defining the interface:

- `.fullName(x)` will return `"Column data table"`.

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

For creating the output:

- `.generateTable(x, envir)` will modify `envir` to contain the relevant data.frame for display, while returning a character vector of commands required to produce that data.frame. Each row of the data.frame should correspond to a column of the SummarizedExperiment.

For documentation:

- `.definePanelTour(x)` returns an data.frame containing the steps of a panel-specific tour.

Unless explicitly specialized above, all methods from the parent class Panel are also available.

### Author(s)

Aaron Lun

### Examples

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

    x <- ColumnDataTable()
    x[["Selected"]]
    x[["Selected"]] <- "SOME_SAMPLE_NAME"

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

    library(scater)
    sce <- mockSCE()

    # Search column refinement works as expected.
    sce0 <- .cacheCommonInfo(x, sce)
    .refineParameters(x, sce0)

[Package iSEE version 2.4.0 Index]