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Assess the stability for Graph Building Parameters

Source: R/stability-2-graph-construction.R
assess_nn_stability.Rd

Evaluates clustering stability when changing the values of different parameters involved in the graph building step, namely the base embedding, the graph type and the number of neighbours.

Usage

assess_nn_stability(
  embedding,
  n_neigh_sequence,
  n_repetitions = 100,
  seed_sequence = NULL,
  graph_reduction_type = "PCA",
  ecs_thresh = 1,
  graph_type = 2,
  prune_value = -1,
  clustering_algorithm = 1,
  clustering_arguments = list(),
  umap_arguments = list()
)

Arguments

embedding

A matrix associated with a PCA embedding. Embeddings from other dimensionality reduction techniques (such as LSI) can be used.

n_neigh_sequence

A sequence of the number of nearest neighbours.

n_repetitions

The number of repetitions of applying the pipeline with different seeds; ignored if seed_sequence is provided by the user.

seed_sequence

A custom seed sequence; if the value is NULL, the sequence will be built starting from 1 with a step of 100.

graph_reduction_type

The graph reduction type, denoting if the graph should be built on either the PCA or the UMAP embedding.

ecs_thresh

The ECS threshold used for merging similar clusterings.

graph_type

Argument indicating whether the graph should be unweighted (0), weighted (1) or both (2).

prune_value

Argument indicating whether to prune the SNN graph. If the value is 0, the graph won't be pruned. If the value is between 0 and 1, the edges with weight under the pruning value will be removed. If the value is -1, the highest pruning value will be calculated automatically and used.

clustering_algorithm

An index indicating which community detection algorithm will be used: Louvain (1), Louvain refined (2), SLM (3) or Leiden (4). More details can be found in the Seurat's FindClusters function.

clustering_arguments

A list of arguments that will be passed to the clustering algorithm. See the FindClusters function in Seurat for more details.

umap_arguments

Additional arguments passed to the the uwot::umap method.

Value

A list having three fields:

  • n_neigh_k_corresp - list containing the number of the clusters obtained by running the pipeline multiple times with different seed, number of neighbours and graph type (weighted vs unweigted)

  • n_neigh_ec_consistency - list containing the EC consistency of the partitions obtained at multiple runs when changing the number of neighbours or the graph type

  • n_different_partitions - the number of different partitions obtained by each number of neighbours

Examples

set.seed(2024)
# create an artificial PCA embedding
pca_emb <- matrix(runif(100 * 30), nrow = 100, byrow = TRUE)
rownames(pca_emb) <- as.character(1:100)
colnames(pca_emb) <- paste0("PC_", 1:30)

nn_stability_obj <- assess_nn_stability(
    embedding = pca_emb,
    n_neigh_sequence = c(10, 15, 20),
    n_repetitions = 10,
    graph_reduction_type = "PCA",
    clustering_algorithm = 1
)
plot_n_neigh_ecs(nn_stability_obj)