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Run MDS (multi-dimensional scaling)

Source: R/RunMDS.R
RunMDS.Rd

Run MDS (multi-dimensional scaling)

Usage

RunMDS(object, ...)

# S3 method for class 'Seurat'
RunMDS(
  object,
  assay = NULL,
  layer = "data",
  features = NULL,
  nmds = 50,
  dist.method = "euclidean",
  mds.method = "cmdscale",
  rev.mds = FALSE,
  reduction.name = "mds",
  reduction.key = "MDS_",
  verbose = TRUE,
  seed.use = 11,
  ...
)

# S3 method for class 'Assay'
RunMDS(
  object,
  assay = NULL,
  layer = "data",
  features = NULL,
  nmds = 50,
  dist.method = "euclidean",
  mds.method = "cmdscale",
  rev.mds = FALSE,
  reduction.key = "MDS_",
  verbose = TRUE,
  seed.use = 11,
  ...
)

# Default S3 method
RunMDS(
  object,
  assay = NULL,
  layer = "data",
  nmds = 50,
  dist.method = "euclidean",
  mds.method = "cmdscale",
  rev.mds = FALSE,
  reduction.key = "MDS_",
  verbose = TRUE,
  seed.use = 11,
  ...
)

Arguments

object

An object. This can be a Seurat object, an assay object, or a matrix-like object.

...

Additional arguments to be passed to the stats::cmdscale, MASS::isoMDS or MASS::sammon function.

assay

A character string specifying the assay to be used for the analysis. Default is NULL.

layer

A character string specifying the layer to be used for the analysis. Default is "data".

features

A character vector specifying the features to be used for the analysis. Default is NULL, which uses all variable features.

nmds

An integer specifying the number of dimensions to be computed. Default is 50.

dist.method

A character string specifying the distance metric to be used. Currently supported values are "euclidean", "chisquared","kullback", "jeffreys", "jensen", "manhattan", "maximum", "canberra", "minkowski", and "hamming". Default is "euclidean".

mds.method

A character string specifying the MDS algorithm to be used. Currently supported values are "cmdscale", "isoMDS", and "sammon". Default is "cmdscale".

rev.mds

A logical value indicating whether to perform reverse MDS (i.e., transpose the input matrix) before running the analysis. Default is FALSE.

reduction.name

A character string specifying the name of the reduction to be stored in the Seurat object. Default is "mds".

reduction.key

A character string specifying the prefix for the column names of the basis vectors. Default is "MDS_".

verbose

A logical value indicating whether to print verbose output. Default is TRUE.

seed.use

An integer specifying the random seed to be used. Default is 11.

Examples

pancreas_sub <- RunMDS(object = pancreas_sub)
#> Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 't': no method for coercing this S4 class to a vector
CellDimPlot(
  pancreas_sub,
  group.by = "CellType",
  reduction = "mds"
)
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's fill values.