R: Compare clustering methods

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]