Compute a spatial CCC graph

Usage

compute_spatial_ccc_graph(
  spe,
  assay_name = "logcounts",
  ligand,
  receptor,
  expression_min_prop = 0.05,
  spot_dist = calc_spot_dist(spe),
  spot_dist_cutoff = 1.5,
  LRscore_cutoff = 0.5
)

Arguments

spe: SpatialExperiment object
assay_name: assay name in string
ligand: ligand
receptor: receptor
expression_min_prop: minimum proportion of samples with non-zero expression value (default: 0.05)
spot_dist: distances between spots, an output of calc_spot_dist()
spot_dist_cutoff: cutoff value for norm.d in spot distances. Default cutoff is 1.5 and it comes from sqrt(3) ~ 1.73, based on how Visium spot-array is arranged, so by default, only computing nearest neighbors.
LRscore_cutoff: minimum LRscore to keep

Value

a spatial CCC graphs in tidygraph format; spatial CCC graph also include the following graph metrics

graph metrics

For overall graph,
- graph_n_nodes,
- graph_n_edges
- graph_component_count
- graph_motif_count
- graph_diameter
- graph_un_diameter
- graph_mean_dist
- graph_circuit_rank = graph_n_edges - graph_n_nodes + graph_component_count
- graph_reciprocity
- graph_clique_num (sp_ccc_graph assumed as undirected)
- graph_clique_count (sp_ccc_graph assumed as undirected)
For each sub-graph (after group_components())
- group_n_nodes
- group_n_edges
- group_adhesion
- group_motif_count
- group_diameter
- group_un_diameter
- group_mean_dist
- group_girth
- group_circuit_rank
- group_reciprocity