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,
  ...
)

# S3 method for class 'Assay5'
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 stats::cmdscale, MASS::isoMDS or MASS::sammon.
assay: The assay to be used for the analysis. Default is NULL.
layer: The layer to be used for the analysis. Default is "data".
features: The features to be used for the analysis. Default is NULL, which uses all variable features.
nmds: The number of dimensions to be computed. Default is 50.
dist.method: 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: The MDS algorithm to be used. Currently supported values are "cmdscale", "isoMDS", and "sammon". Default is "cmdscale".
rev.mds: Whether to perform reverse MDS (i.e., transpose the input matrix) before running the analysis. Default is FALSE.
reduction.name: The name of the reduction to be stored in the Seurat object. Default is "mds".
reduction.key: The prefix for the column names of the basis vectors. Default is "MDS_".
verbose: Whether to print the message. Default is TRUE.
seed.use: The random seed to be used. Default is 11.

Examples

pancreas_sub <- RunMDS(object = pancreas_sub)
#> Warning: Layer ‘data’ is empty
#> Error in apply(X = data_use[features, ], MARGIN = 1, FUN = stats::var): dim(X) must have a positive length
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.