plot_n_neigh_ecs: Graph construction parameters - ECC facet

In Core-Bioinformatics/ClustAssess: Tools for Assessing Clustering

Graph construction parameters - ECC facet

Description

Display, for all configurations consisting in different number of neighbours, graph types and base embeddings, the EC Consistency of the partitions obtained over multiple runs on an UMAP embedding.

Usage

plot_n_neigh_ecs(nn_ecs_object, boxplot_width = 0.5)

Arguments

nn_ecs_object	An object or a concatenation of objects returned by the get_nn_importance method.
boxplot_width	Used for adjusting the width of the boxplots; the value will be passed to the width argument of the ggplot2::geom_boxplot method.

Value

A ggplot2 object.

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)

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