k_select {musicatk} | R Documentation

## Plots for helping decide number of clusters

### Description

To help decide the number of cluster, three different methods are provided: total within cluster sum of squares, average silhouette coefficient, and gap statistics.

### Usage

    k_select(
      result,
      method = "wss",
      clust.method = "kmeans",
      n = 10,
      proportional = TRUE
    )

### Arguments

`result` | A `musica_result` object generated by a mutational discovery or prediction tool.
`method` | A single character string indicating which statistic to use for plot. Options are "wss" (total within cluster sum of squares), "silhouette" (average silhouette coefficient), and "gap_stat" (gap statistic). Default is "wss".
`clust.method` | A character string indicating clustering method. Options are "kmeans" (default), "hclust" (hierarchical clustering), "hkmeans", "pam", and "clara".
`n` | An integer indicating maximum number of clusters to test. Default is 10.
`proportional` | Logical, indicating if proportional exposure (default) will be used for clustering.

### Value

A ggplot object.

### See Also

fviz_nbclust

### Examples

    data(res_annot)
    set.seed(123)
    #Make an elbow plot
    k_select(res_annot, method = "wss", n = 6)
    #Plot average silhouette coefficient against number of clusters
    k_select(res_annot, method = "silhouette", n = 6)
    #Plot gap statistics against number of clusters
    k_select(res_annot, method = "gap_stat", n = 6)

[Package musicatk version 1.2.0 Index]