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 name to be used. Default is "data".
n_components: An integer specifying the number of TriMap components. Default is 2.
n_inliers: An integer specifying the number of nearest neighbors for forming the nearest neighbor triplets. Default is 12.
n_outliers: An integer specifying the number of outliers for forming the nearest neighbor triplets. Default is 4.
n_random: An integer specifying the 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: A numeric value specifying the learning rate for TriMap. Default is 0.1.
n_iters: An integer specifying the number of iterations for TriMap. Default is 400.
apply_pca: A logical value indicating 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: 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 <- Seurat::FindVariableFeatures(pancreas_sub)
pancreas_sub <- RunTriMap(object = pancreas_sub, features = Seurat::VariableFeatures(pancreas_sub))
#> Error in check_Python("trimap"): could not find function "check_Python"
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.