Conveinience function to run isoMDS on a SingleCellExperiment object.

Source: R/dimension_reduction.R

Conveinience function to run isoMDS on a SingleCellExperiment object.

isomds(object, exprs_values, features = NULL, method = "spearman", ...)

Arguments

object

A SingleCellExperiment object.
exprs_values

String indicating which assay contains the data that should be used to perform isoMDS.
features

A character vector (of feature names), a logical vector or numeric vector (of indices) specifying the features to use for isoMDS. The default of NULL will use all features.
method

A character string specifying the method to be used to calulate a dissimilarity structure using WGCNA::cor.
...

Additional parameters to be passed on to MASS::isoMDS.

Value

A matrix with the k-dimensional embedding.