calculateDiffusionMap {scater}R Documentation

Create a diffusion map from cell-level data

Description

Produce a diffusion map for the cells, based on the data in a SingleCellExperiment object.

Usage

calculateDiffusionMap(x, ...)

## S4 method for signature 'ANY'
calculateDiffusionMap(x, ncomponents = 2, ntop = 500,
  subset_row = NULL, feature_set = NULL, scale = FALSE,
  scale_features = NULL, transposed = FALSE, ...)

## S4 method for signature 'SummarizedExperiment'
calculateDiffusionMap(x, ...,
  exprs_values = "logcounts")

## S4 method for signature 'SingleCellExperiment'
calculateDiffusionMap(x, ...,
  exprs_values = "logcounts", dimred = NULL, use_dimred = NULL,
  n_dimred = NULL)

runDiffusionMap(x, ..., altexp = NULL, name = "DiffusionMap")

Arguments

x

For calculateDiffusionMap, a numeric matrix of log-expression values where rows are features and columns are cells. Alternatively, a SummarizedExperiment or SingleCellExperiment containing such a matrix.

For runDiffusionMap, a SingleCellExperiment object.

...

For the calculateDiffusionMap generic, additional arguments to pass to specific methods. For the ANY method, additional arguments to pass to DiffusionMap. For the SummarizedExperiment and SingleCellExperiment methods, additional arguments to pass to the ANY method.

For runDiffusionMap, additional arguments to pass to calculateDiffusionMap.

ncomponents

Numeric scalar indicating the number of UMAP dimensions to obtain.

ntop

Numeric scalar specifying the number of features with the highest variances to use for PCA, see ?"scater-red-dim-args".

subset_row

Vector specifying the subset of features to use for PCA, see ?"scater-red-dim-args".

feature_set

Deprecated, same as subset_row.

scale

Logical scalar, should the expression values be standardised? See ?"scater-red-dim-args" for details.

scale_features

Deprecated, same as scale but with a different default.

transposed

Logical scalar, is x transposed with cells in rows? See ?"scater-red-dim-args" for details.

exprs_values

Integer scalar or string indicating which assay of x contains the expression values, see ?"scater-red-dim-args".

dimred

String or integer scalar specifying the existing dimensionality reduction results to use, see ?"scater-red-dim-args".

use_dimred

Deprecated, same as dimred.

n_dimred

Integer scalar or vector specifying the dimensions to use if dimred is specified, see ?"scater-red-dim-args".

altexp

String or integer scalar specifying an alternative experiment to use to compute the PCA, see ?"scater-red-dim-args".

name

String specifying the name to be used to store the result in the reducedDims of the output.

Details

The function DiffusionMap is used internally to compute the diffusion map. The behaviour of DiffusionMap seems to be non-deterministic, in a manner that is not responsive to any set.seed call. The reason for this is unknown.

Value

For calculateDiffusionMap, a matrix is returned containing the diffusion map coordinates for each cell (row) and dimension (column).

For runDiffusionMap, a modified x is returned that contains the diffusion map coordinates in reducedDim(x, name).

Author(s)

Aaron Lun, based on code by Davis McCarthy

References

Haghverdi L, Buettner F, Theis FJ (2015). Diffusion maps for high-dimensional single-cell analysis of differentiation data. Bioinformatics 31(18), 2989-2998.

See Also

DiffusionMap, to perform the underlying calculations.

plotDiffusionMap, to quickly visualize the results.

?"scater-red-dim-args", for a full description of various options.

Examples

example_sce <- mockSCE()
example_sce <- logNormCounts(example_sce)

example_sce <- runDiffusionMap(example_sce, scale_features=NULL)
reducedDimNames(example_sce)
head(reducedDim(example_sce))

[Package scater version 1.14.0 Index]