runUMAP: UMAP analysis

In supatt-lab/SingCellaR: SingCellaR: an integrative analysis tool for single-cell RNA sequencing (scRNA-seq) data

UMAP analysis

Description

UMAP analysis

Usage

runUMAP(
  object,
  dim_reduction_method = c("pca", "nnmf", "lsi"),
  useIntegrativeEmbeddings = FALSE,
  integrative_method = c("combat", "seurat", "harmony", "supervised_harmony", "liger"),
  umap_method = c("uwot"),
  n.dims.use = 50,
  n.neighbors = 30,
  n.seed = 1,
  uwot.metric = "cosine",
  uwot.n.epochs = NULL,
  uwot.learning.rate = 1,
  uwot.min.dist = 0.25,
  uwot.spread = 1,
  uwot.set.op.mix.ratio = 1,
  uwot.local.connectivity = 1L,
  uwot.repulsion.strength = 1,
  uwot.negative.sample.rate = 5,
  uwot.a = NULL,
  uwot.b = NULL,
  uwot.metric.kwds = NULL,
  uwot.angular.rp.forest = FALSE,
  uwot.verbose = TRUE,
  uwot.save.model = FALSE,
  uwot.save.file = "uwot.out.rdata"
)

Arguments

object	The SingCellaR object.
dim_reduction_method	Dimensional reduction method name that specifies the embedding matrix.
useIntegrativeEmbeddings	is logical, if TRUE the embedding matrix genereated from integrative analysis will be used.
integrative_method	The name of an integrative method.
umap_method	The seleced UMAP analysis method.
n.dims.use	The number of dimensions as the input.
n.neighbors	The size of local neighborhood (in terms of number of neighboring sample points) used for manifold approximation. Default 30
n.seed	The number of seed.
uwot.metric	uwot's distance metric. Default 'cosine'.
uwot.spread	uwot spread parameter. Default 1.0
uwot.set.op.mix.ratio	uwot set.op.mix.ratio parameter. Default 1.0
uwot.local.connectivity	uwot local connectivity parameter. Default 1L
uwot.repulsion.strength	uwot repulsion.strength parameter. Default 1
uwot.negative.sample.rate	uwot negative.sample.rate parameter. Default 5
uwot.a	uwot a parameter.
uwot.b	uwot b parameter.
uwot.metric.kwds	uwot metric.kwds parameter.
uwot.angular.rp.forest	is the logical of uwot angular.rp.forest.
uwot.verbose	is logical for uwot verbose parameter.
uwot.save.model	is the logical. If TRUE, the uwot model will be saved.
uwot.save.file	The file name of uwot model to be saved.

supatt-lab/SingCellaR documentation built on Aug. 24, 2023, 5:49 p.m.