Description Getters Single-result setter Other setters Author(s) Examples
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.
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
.
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.
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
.
Aaron Lun and Kevin Rue-Albrecht
1 2 3 4 5 6 7 8 9 10 | example(SingleCellExperiment, echo=FALSE)
reducedDim(sce, "PCA")
reducedDim(sce, "tSNE")
reducedDims(sce)
reducedDim(sce, "PCA") <- NULL
reducedDims(sce)
reducedDims(sce) <- SimpleList()
reducedDims(sce)
|
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