runFA2_ForceDirectedGraph: ForceAtlas2 analysis

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

ForceAtlas2 analysis

Description

ForceAtlas2 analysis

Usage

runFA2_ForceDirectedGraph(
  object,
  dim_reduction_method = c("pca", "nnmf", "lsi"),
  useIntegrativeEmbeddings = F,
  integrative_method = c("combat", "seurat", "harmony", "supervised_harmony"),
  knn.metric = c("euclidean", "cosine"),
  n.dims.use = 30,
  n.neighbors = 5,
  n.seed = 1,
  knn.n_trees = 50,
  knn.n_threads = 1,
  fa2_n_iter = 1000,
  fa2_edgeWeightInfluence = 1,
  fa2_barnesHutTheta = 2,
  fa2_scalingRatio = 1,
  fa2_gravity = 0.05,
  fa2_jitterTolerance = 1
)

Arguments

object	The SingCellaR object.
useIntegrativeEmbeddings	is logical, if TRUE the embedding matrix genereated from integrative analysis will be used.
integrative_method	The name of an integrative method.
knn.metric	Type of distance metric to use to find nearest neighbors.
n.dims.use	The number of dimensions as the input. Default 30
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 set seed.
knn.n_trees	The number of trees for building the annoy index. Default 50
knn.n_threads	The number of threads. Default 1
fa2_n_iter	The FA2 number of iterations. Default 1000
fa2_edgeWeightInfluence	The FA2 edgeWeightInfluence parameter. Default 1
fa2_barnesHutTheta	The FA2 barnesHutTheta paramenter. Default 2
fa2_scalingRatio	The FA2 scalingRatio parameter. Default 1
fa2_gravity	The FA2 gravity parameter. Default 0.05
fa2_jitterTolerance	The FA2 jitterTolerance parameter. Default 1

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