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Run TriMap (Large-scale Dimensionality Reduction Using Triplets)

Source: R/RunTriMap.R
RunTriMap.Rd

Run TriMap (Large-scale Dimensionality Reduction Using Triplets)

Usage

RunTriMap(object, ...)

# S3 method for class 'Seurat'
RunTriMap(
  object,
  reduction = "pca",
  dims = NULL,
  features = NULL,
  assay = NULL,
  layer = "data",
  n_components = 2,
  n_inliers = 12,
  n_outliers = 4,
  n_random = 3,
  distance_method = "euclidean",
  lr = 0.1,
  n_iters = 400,
  apply_pca = TRUE,
  opt_method = "dbd",
  reduction.name = "trimap",
  reduction.key = "TriMap_",
  verbose = TRUE,
  seed.use = 11L,
  ...
)

# Default S3 method
RunTriMap(
  object,
  assay = NULL,
  n_components = 2,
  n_inliers = 12,
  n_outliers = 4,
  n_random = 3,
  distance_method = "euclidean",
  lr = 0.1,
  n_iters = 400,
  apply_pca = TRUE,
  opt_method = "dbd",
  reduction.key = "TriMap_",
  verbose = TRUE,
  seed.use = 11L,
  ...
)

Arguments

object

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

...

Additional arguments to be passed to the trimap.TRIMAP function.

reduction

A character string specifying the reduction to be used. Default is "pca".

dims

An integer vector specifying the dimensions to be used. Default is NULL.

features

A character vector specifying the features to be used. Default is NULL.

assay

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

layer

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

n_components

A number of TriMap components. Default is 2.

n_inliers

A number of nearest neighbors for forming the nearest neighbor triplets. Default is 12.

n_outliers

A number of outliers for forming the nearest neighbor triplets. Default is 4.

n_random

A number of random triplets per point. Default is 3.

distance_method

A character string specifying the distance metric for TriMap. Options are: "euclidean", "manhattan", "angular", "cosine", "hamming". Default is "euclidean".

lr

The learning rate for TriMap. Default is 0.1.

n_iters

A number of iterations for TriMap. Default is 400.

apply_pca

Whether to apply PCA before the nearest-neighbor calculation. Default is TRUE.

opt_method

A character string specifying the optimization method for TriMap. Options are: "dbd", "sd", "momentum". Default is "dbd".

reduction.name

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

reduction.key

A character string specifying the prefix for the column names of the TriMap embeddings. Default is "TriMap_".

verbose

Whether to print the message. Default is TRUE.

seed.use

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

Examples

pancreas_sub <- Seurat::FindVariableFeatures(pancreas_sub)
#> Finding variable features for layer counts
pancreas_sub <- RunTriMap(
  object = pancreas_sub,
  features = SeuratObject::VariableFeatures(pancreas_sub)
)
#> Warning: Layer ‘data’ is empty
#> Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 't': subscript out of bounds
CellDimPlot(
  pancreas_sub,
  group.by = "CellType",
  reduction = "trimap"
)
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's fill values.