R: Relationship Between Number of Nearest Neighbors and Number...

plot_n_neigh_k_correspondence {ClustAssess} | R Documentation

## 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)

[Package ClustAssess version 0.3.0 Index]