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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, a matrix-like object, a Neighbor object, or a Graph object.

...

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

reduction

Which dimensionality reduction to use. Default is "pca".

dims

The dimensions to be used. Default is NULL.

features

A character vector of features to use. Default is NULL.

assay

Which assay to use. If NULL, the default assay of the Seurat object will be used.

layer

Which layer to use. 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

Random seed for reproducibility. Default is 11.

Examples

if (FALSE) { # \dontrun{
data(pancreas_sub)
pancreas_sub <- standard_scop(pancreas_sub)
pancreas_sub <- RunTriMap(
  object = pancreas_sub,
  features = SeuratObject::VariableFeatures(pancreas_sub)
)
CellDimPlot(
  pancreas_sub,
  group.by = "CellType",
  reduction = "trimap"
)
} # }