plot_n_neigh_k_correspondence: Relationship Between Number of Nearest Neighbours and Number...

In Core-Bioinformatics/ClustAssess: Tools for Assessing Clustering

Relationship Between Number of Nearest Neighbours and Number of Clusters

Description

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

Usage

plot_n_neigh_k_correspondence(nn_object_n_clusters)

Arguments

nn_object_n_clusters

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

Value

A ggplot2 object with the distributions displayed as boxplots.

Note

The number of clusters 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("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_k_correspondence(nn_stability_obj)

Core-Bioinformatics/ClustAssess documentation built on Nov. 14, 2024, 6:33 p.m.