Combine kNN graphs to large cell-gene adjecency matrix

Builds a single adjacency matrix consisting of cells and genes from 4 seperate sub kNN-graphs.

Usage

create_bigraph(
  caobj,
  k_c,
  k_g,
  k_cg,
  k_gc,
  loops = FALSE,
  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_c

k for cell-cell kNN, integer.

k_g

k for gene-gene kNN, integer.

k_cg

k for cell-gene kNN, integer.

k_gc

k for gene-cell kNN, interger.

loops

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

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

Adjacency matrix of type dgCMatrix. The combined adjacency matrix consists of the cell-cell graph, gene-gene graph and cell-gene/gene-cell graph.

Details

method should be a kNN algorithm defined by BiocNeighbors::BiocNeighborParam. For exact kNN search use BiocNeighbors::KmknnParam() or BiocNeighbors::VptreeParam().