build_knn_graph_nn2: Build kNN graph using RANN::nn2 (used in '"build_knn_graph"')

In SuperCell: Simplification of scRNA-Seq Data by Merging Together Similar Cells

Build kNN graph using RANN::nn2 (used in "build_knn_graph")

Description

Build kNN graph using RANN::nn2 (used in "build_knn_graph")

Usage

build_knn_graph_nn2(
  X,
  k = min(5, ncol(X)),
  mode = "all",
  DoSNN = FALSE,
  which.snn = c("bluster", "dbscan"),
  pruning = NULL,
  kmin = 0,
  ...
)

Arguments

X	matrix of coordinates (rows are samples and cols are coordinates)
k	kNN parameter
mode	mode of graph_from_adj_list ('all' – undirected graph, 'out' – directed graph)
DoSNN	whether to apply shared nearest neighbors (default is FALSE)
which.snn	whether to use neighborsToSNNGraph or sNN for sNN graph construction
pruning	quantile to perform edge pruning (default is NULL - no pruning applied) based on PCA distance distribution
kmin	keep at least kmin edges in single-cell graph when pruning applied (idnored if is.null(pruning))
...	other parameters of neighborsToSNNGraph or sNN

Value

a list with components

• graph.knn - igraph object

SuperCell documentation built on Oct. 25, 2024, 5:07 p.m.