calculateMDS {scater}R Documentation

Perform MDS on cell-level data

Description

Perform multi-dimensional scaling (MDS) on cells, based on the data in a SingleCellExperiment object.

Usage

calculateMDS(x, ...)

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

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

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

runMDS(x, ..., altexp = NULL, name = "MDS")

Arguments

x

For calculateMDS, 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 runMDS, a SingleCellExperiment object.

...

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

For runMDS, additional arguments to pass to calculateMDS.

ncomponents

Numeric scalar indicating the number of MDS?g 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.

method

String specifying the type of distance to be computed between cells.

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 cmdscale is used internally to compute the MDS components.

Value

For calculateMDS, a matrix is returned containing the MDS coordinates for each cell (row) and dimension (column).

For runMDS, a modified x is returned that contains the MDS coordinates in reducedDim(x, name).

Author(s)

Aaron Lun, based on code by Davis McCarthy

See Also

cmdscale, to perform the underlying calculations.

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

[Package scater version 1.14.0 Index]