Clarification on Directed vs. Undirected SNN Graph in Seurat Clustering

[tim-meese]

Dear Seurat Developers,

I have a question regarding clustering in the Seurat package. From my understanding, Seurat performs clustering on the shared nearest neighbors (SNN) graph. Could you please clarify whether this graph is directed or undirected?

I intend to apply methods from the igraph package to the SNN graph and need to construct an igraph object. In the Seurat source code, I found the function RunLeiden(), which constructs an igraph object using graph_from_adjacency_matrix(adjmatrix = object, weighted = TRUE), resulting in a directed graph. However, I am unsure if the SNN graph itself is directed.

Thank you for your assistance.

Best regards,
Tim