plot_n_neigh_k_correspondence {ClustAssess}

Relationship Between Number of Nearest Neighbors and Number of Clusters

Description

Display the distribution of the number of clusters obtained for each number of neighbors 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(2021)
# create an artificial expression matrix
expr_matrix = matrix(runif(100*10), nrow = 100)
rownames(expr_matrix) = as.character(1:100)

nn_importance_obj = get_nn_importance(object = expr_matrix,
    n_neigh_sequence = c(2,5),
    n_repetitions = 5,
    graph_reduction_type = "PCA",
    algorithm = 1,
    transpose = FALSE, # the matrix is already observations x features, so we won't transpose it
    # the following parameter is used by the irlba function and is not mandatory
    nv = 2)
plot_n_neigh_k_correspondence(nn_importance_obj)