plot_connected_comps_evolution {ClustAssess} | R Documentation |
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 |
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)
[Package ClustAssess version 1.1.0 Index]