cache-utils {iSEE} | R Documentation

## Caching utilities

### Description

Utility functions to be used in a `.cacheCommonInfo` method, usually to identify names of elements of the SummarizedExperiment for later use in `.defineInterface` to populate the user interface.

### Usage

    .findAtomicFields(x)

    .whichGroupable(x, max_levels = Inf)

    .whichNumeric(x)

    .isAssayNumeric(se, i)

### Arguments

`x` | A data.frame or DataFrame, most typically the `rowData` or `colData`.
`max_levels` | Integer scalar specifying the maximum number unique values for `x` to be categorical.
`se` | The SummarizedExperiment object.
`i` | An integer scalar or string specifying the assay of interest in `se`.

### Details

`.findAtomicFields` is necessary as many of the widgets used by `iSEE` (e.g., `ggplot`, `datatable`) do not know how to handle more complex types being stored as columns. Similarly, `.whichNumeric` and `.whichGroupable` can be used to specify options for visualization modes that only make sense for continuous or discrete variables respectively (e.g., sizing, faceting).

### Value

For `.findAtomicFields`, a character vector of names of columns in `x` containing atomic R types.

For `.whichNumeric`, an integer vector containing the indices of the numeric columns.

For `.whichGroupable`, an integer vector containing the indices of the categorical columns.

For `.isAssayNumeric`, a logical scalar indicating whether the specified assay as numeric.

### Author(s)

Aaron Lun, Kevin Rue-Albrecht, Charlotte Soneson

### Examples

    x <- DataFrame(
        A = rnorm(10),
        B = sample(letters, 10),
        DataFrame = I(DataFrame(
            C = rnorm(10),
            D = sample(letters, 10)
        ))
    )

    .findAtomicFields(x)
    .whichGroupable(x)
    .whichNumeric(x)

[Package iSEE version 2.6.0 Index]