compare_clustering_methods {simplifyEnrichment} | R Documentation

## Compare clustering methods

### Description

Compare clustering methods

### Usage

    compare_clustering_methods(mat, method = setdiff(all_clustering_methods(), "mclust"),
        plot_type = c("mixed", "heatmap"), nrow = 3, verbose = TRUE)

### Arguments

`mat` | The similarity matrix.
`method` | Which methods to compare. All available methods are in `all_clustering_methods`. A value of `all` takes all available methods. By default `mclust` is excluded because its long runtime.
`plot_type` | See explanation in `cmp_make_plot`.
`nrow` | Number of rows of the layout when `plot_type` is set to `heatmap`.
`verbose` | Whether to print messages.

### Details

The function compares following clustering methods by default:

`kmeans`

  see `cluster_by_kmeans`.

`dynamicTreeCut`

  see `cluster_by_dynamicTreeCut`.

`mclust`

  see `cluster_by_mclust`. By default it is not included.

`apcluster`

  see `cluster_by_apcluster`.

`hdbscan`

  see `cluster_by_hdbscan`.

`fast_greedy`

  see `cluster_by_igraph`.

`leading_eigen`

  see `cluster_by_igraph`.

`louvain`

  see `cluster_by_igraph`.

`walktrap`

  see `cluster_by_igraph`.

`MCL`

  see `cluster_by_MCL`.

`binary_cut`

  see `binary_cut`.

This functon is basically a wrapper function. It calls the following two functions:

- `cmp_make_clusters`: applies clustering with different methods.

- `cmp_make_plot`: makes the plots.

### Value

No value is returned.

### Examples

    ## Not run:
    mat = readRDS(system.file("extdata", "random_GO_BP_sim_mat.rds",
        package = "simplifyEnrichment"))
    compare_clustering_methods(mat)
    compare_clustering_methods(mat, plot_type = "heatmap")

    ## End(Not run)

[Package simplifyEnrichment version 1.2.0 Index]