plot_connected_comps_evolution: Relationship Between Number of Nearest Neighbours and Graph...

In Core-Bioinformatics/ClustAssess: Tools for Assessing Clustering

Relationship Between Number of Nearest Neighbours and Graph Connectivity

Description

Display the distribution of the number connected components obtained for each number of neighbours across random seeds.

Usage

plot_connected_comps_evolution(nn_conn_comps_object)

Arguments

nn_conn_comps_object

An object or a concatenation of objects returned by the get_nn_conn_comps method.

Value

A ggplot2 object with boxplots for the connected component distributions.

Note

The number of connected components is displayed on a logarithmic scale.

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("PCA_", 1:30)

nn_conn_comps_obj <- get_nn_conn_comps(
    embedding = pca_emb,
    n_neigh_sequence = c(2, 5),
    n_repetitions = 3,
    # arguments that are passed to the uwot function
    umap_arguments = list(
        min_dist = 0.3,
        metric = "cosine"
    )
)
plot_connected_comps_evolution(nn_conn_comps_obj)

Core-Bioinformatics/ClustAssess documentation built on Dec. 19, 2024, 8:19 p.m.