RunUMAP2: Run UMAP (Uniform Manifold Approximation and Projection)

In zh542370159/SCP: Single Cell Pipeline

Run UMAP (Uniform Manifold Approximation and Projection)

Description

Run UMAP (Uniform Manifold Approximation and Projection)

Usage

RunUMAP2(object, ...)

## S3 method for class 'Seurat'
RunUMAP2(
  object,
  reduction = "pca",
  dims = NULL,
  features = NULL,
  neighbor = NULL,
  graph = NULL,
  assay = NULL,
  slot = "data",
  umap.method = "uwot",
  reduction.model = NULL,
  n_threads = NULL,
  return.model = FALSE,
  n.neighbors = 30L,
  n.components = 2L,
  metric = "cosine",
  n.epochs = 200L,
  spread = 1,
  min.dist = 0.3,
  set.op.mix.ratio = 1,
  local.connectivity = 1L,
  negative.sample.rate = 5L,
  a = NULL,
  b = NULL,
  learning.rate = 1,
  repulsion.strength = 1,
  reduction.name = "umap",
  reduction.key = "UMAP_",
  verbose = TRUE,
  seed.use = 11L,
  ...
)

## Default S3 method:
RunUMAP2(
  object,
  assay = NULL,
  umap.method = "uwot",
  reduction.model = NULL,
  n_threads = NULL,
  return.model = FALSE,
  n.neighbors = 30L,
  n.components = 2L,
  metric = "cosine",
  n.epochs = 200L,
  spread = 1,
  min.dist = 0.3,
  set.op.mix.ratio = 1,
  local.connectivity = 1L,
  negative.sample.rate = 5L,
  a = NULL,
  b = NULL,
  learning.rate = 1,
  repulsion.strength = 1,
  reduction.key = "UMAP_",
  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.
...	Unused argument.
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.
neighbor	A character string specifying the name of the Neighbor object to be used. Default is NULL.
graph	A character string specifying the name of the Graph object to be used. Default is NULL.
assay	A character string specifying the assay to be used. Default is NULL.
slot	A character string specifying the slot name to be used. Default is "data".
umap.method	A character string specifying the UMAP method to be used. Options are "naive" and uwot". Default is "uwot".
reduction.model	A DimReduc object containing a pre-trained UMAP model. Default is NULL.
return.model	A logical value indicating whether to return the UMAP model. Default is FALSE.
n.neighbors	An integer specifying the number of nearest neighbors to be used. Default is 30.
n.components	An integer specifying the number of UMAP components. Default is 2.
metric	A character string specifying the metric or a function to be used for distance calculations. When using a string, available metrics are: euclidean, manhattan. Other available generalized metrics are: cosine, pearson, pearson2. Note the triangle inequality may not be satisfied by some generalized metrics, hence knn search may not be optimal. When using metric.function as a function, the signature must be function(matrix, origin, target) and should compute a distance between the origin column and the target columns. Default is "cosine".
n.epochs	An integer specifying the number of iterations performed during layout optimization for UMAP. Default is 200.
spread	A numeric value specifying the spread parameter for UMAP, used during automatic estimation of a/b parameters. Default is 1.
min.dist	A numeric value specifying the minimum distance between UMAP embeddings, determines how close points appear in the final layout. Default is 0.3.
set.op.mix.ratio	Interpolate between (fuzzy) union and intersection as the set operation used to combine local fuzzy simplicial sets to obtain a global fuzzy simplicial sets. Both fuzzy set operations use the product t-norm. The value of this parameter should be between 0.0 and 1.0; a value of 1.0 will use a pure fuzzy union, while 0.0 will use a pure fuzzy intersection.
local.connectivity	An integer specifying the local connectivity, used during construction of fuzzy simplicial set. Default is 1.
negative.sample.rate	An integer specifying the negative sample rate for UMAP optimization. Determines how many non-neighbor points are used per point and per iteration during layout optimization. Default is 5.
a	A numeric value specifying the parameter a for UMAP optimization. Contributes to gradient calculations during layout optimization. When left at NA, a suitable value will be estimated automatically. Default is NULL.
b	A numeric value specifying the parameter b for UMAP optimization. Contributes to gradient calculations during layout optimization. When left at NA, a suitable value will be estimated automatically. Default is NULL.
learning.rate	A numeric value specifying the initial value of "learning rate" of layout optimization. Default is 1.
repulsion.strength	A numeric value determines, together with alpha, the learning rate of layout optimization. Default is 1.
reduction.name	A character string specifying the name of the reduction to be stored in the Seurat object. Default is "umap".
reduction.key	A character string specifying the prefix for the column names of the UMAP embeddings. Default is "UMAP_".
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 <- RunUMAP2(object = pancreas_sub, features = Seurat::VariableFeatures(pancreas_sub))
CellDimPlot(pancreas_sub, group.by = "CellType", reduction = "umap")

zh542370159/SCP documentation built on Nov. 22, 2023, 2:34 a.m.