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Create SNN-graph from caobj

make_SNN.Rd

Builds a shared nearest neighbour graph (SNN) from a "cacomp" object.

Usage

make_SNN(
  caobj,
  k,
  SNN_prune = 1/15,
  loops = FALSE,
  mode = "out",
  select_genes = TRUE,
  prune_overlap = TRUE,
  overlap = 0.2,
  calc_gene_cell_kNN = FALSE,
  marker_genes = NULL,
  method = BiocNeighbors::KmknnParam(),
  BPPARAM = BiocParallel::SerialParam()
)

Arguments

caobj

A cacomp object with standard and principal coordinates calculated.

k

Either an integer (same k for all subgraphs) or a vector of exactly four integers specifying in this order:

  • k_c for the cell-cell kNN-graph

  • k_g for the gene-gene kNN-graph

  • k_cg for the cell-gene kNN-graph

  • k_gc for the gene-cell kNN-graph.

SNN_prune

numeric. Value between 0-1. Sets cutoff of acceptable jaccard similarity scores for neighborhood overlap of vertices in SNN. Edges with values less than this will be set as 0. The default value is 1/15.

loops

TRUE/FALSE. If TRUE self-loops are allowed, otherwise not.

mode

The type of neighboring vertices to use for calculating similarity scores(Jaccard Index). Three options: "out", "in" and "all":

  • "out": Selecting neighbouring vertices by out-going edges;

  • "in": Selecting neighbouring vertices by in-coming edges;

  • "all": Selecting neigbouring vertices by both in-coming and out-going edges.

select_genes

TRUE/FALSE. Should genes be selected by whether they have an edge in the cell-gene kNN graph?

prune_overlap

TRUE/FALSE. If TRUE edges to genes that share less than overlap of genes with the nearest neighbours of the cell are removed. Pruning is only performed if select_genes = TRUE.

overlap

Numeric between 0 and 1. Overlap cutoff applied if prune_overlap = TRUE.

calc_gene_cell_kNN

TRUE/FALSE. If TRUE a cell-gene graph is calculated by choosing the k_gc nearest cells for each gene. If FALSE the cell-gene graph is transposed.

marker_genes

character. Optional. Names of known marker genes that should be excempt from any pruning on the graph and be kept.

method

BiocNeighbors::BiocNeighborParam object specifying the algorithm to use. see Details.

BPPARAM

BiocParallel settings parameter. By default single core BiocParallel::SerialParam() but other parameters can be passed.

Value

A sparse adjacency Matrix of type "dgCMatrix". The values in the matrix are the Jaccard similarity between nodes in the graph. The range between 0 and 1, with 0 meaning that no edges are shared between nodes, wheras 1 means all edges are shared between nodes.

See also

Other biclustering: caclust, run_leiden(), run_spectral()