Generates the sNN graph for igraph

This function takes a kNN matrix and generates the inputs for an SNN graph based on it.

Usage

rs_sc_snn(knn_mat, snn_method, limited_graph, pruning, verbose)

Arguments

knn_mat

Integer matrix. Rows represent cells and the columns represent the neighbours.

snn_method

String. Which method to use to calculate the similarity. Choice of c("jaccard", "rank").

limited_graph

Boolean. Shall the sNNs only be calculated between direct neighbours in the graph, or between all possible combinations.

pruning

Float. Below which value for the Jaccard similarity to prune the weight to 0.

verbose

Boolean. Controls verbosity of the function.

Value

A list with the following items:

• edges - sNN edges as edge pairs.

• weights - sNN weights of the pairs above.