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Caching utilities

Source: R/utils_class.R
cache-utils.Rd

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.

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.

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).

Author

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)
#> [1] "A" "B"
.whichGroupable(x)
#>         B DataFrame 
#>         2         3 
.whichNumeric(x)
#> A 
#> 1