reducedDims {SingleCellExperiment} | R Documentation

## Reduced dimensions methods

### Description

Methods to get or set dimensionality reduction results in a SingleCellExperiment object. These are typically used to store and retrieve low-dimensional representations of single-cell datasets. Each row of a reduced dimension result is expected to correspond to a column of the SingleCellExperiment object.

### Getters

In the following examples, `x` is a SingleCellExperiment object.

`reducedDim(x, type, withDimnames=TRUE)`:

  Retrieves a matrix (or matrix-like object) containing reduced dimension coordinates for cells (rows) and dimensions (columns). `type` is either a string specifying the name of the dimensionality reduction result in `x` to retrieve, or a numeric scalar specifying the index of the desired result. If `withDimnames=TRUE`, row names of the output matrix are replaced with the column names of `x`.

`reducedDimNames(x)`:

  Returns a character vector containing the names of all dimensionality reduction results in `x`. This is guaranteed to be of the same length as the number of results, though the names may not be unique.

`reducedDims(x, withDimnames=TRUE)`:

  Returns a named List of matrices containing one or more dimensionality reduction results. Each result is a matrix (or matrix-like object) with the same number of rows. If `withDimnames=TRUE`, row names of each matrix are replaced with the column names of `x`.

### Single-result setter

`reducedDim(x, type) <- value` will add or replace a dimensionality reduction result in a SingleCellExperiment object `x`. The value of `type` determines how the result is added or replaced:

- If `type` is missing, `value` is assigned to the first result. If the result already exists, its name is preserved; otherwise it is given a default name `"unnamed1"`.

- If `type` is a numeric scalar, it must be within the range of existing results, and `value` will be assigned to the result at that index.

- If `type` is a string and a result exists with this name, `value` is assigned to to that result. Otherwise a new result with this name is append to the existing list of results.

`value` is expected to be a matrix or matrix-like object with number of rows equal to `ncol(x)`. Alternatively, if `value` is `NULL`, the result corresponding to `type` is removed from the object.

### Other setters

In the following examples, `x` is a SingleCellExperiment object.

`reducedDims(x) <- value`:

  Replaces all dimensionality reduction results in `x` with those in `value`. The latter should be a list-like object containing any number of matrices or matrix-like objects with number of rows equal to `ncol(x)`.

  If `value` is named, those names will be used to name the dimensionality reduction results in `x`. Otherwise, unnamed results are assigned default names prefixed with `"unnamed"`.

  If `value` is `NULL`, all dimensionality reduction results in `x` are removed.

`reducedDimNames(x) <- value`:

  Replaces all names for dimensionality reduction results in `x` with a character vector `value`. This should be of length equal to the number of results currently in `x`.

### Author(s)

Aaron Lun and Kevin Rue-Albrecht

### Examples

    example(SingleCellExperiment, echo=FALSE)
    reducedDim(sce, "PCA")
    reducedDim(sce, "tSNE")
    reducedDims(sce)

    reducedDim(sce, "PCA") <- NULL
    reducedDims(sce)

    reducedDims(sce) <- SimpleList()
    reducedDims(sce)

[Package SingleCellExperiment version 1.9.3 Index]