compare_clustering_methods: Compare clustering methods

In jokergoo/simplifyGO: Simplify Functional Enrichment Results

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.

pam

see cluster_by_pam.

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.

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)

jokergoo/simplifyGO documentation built on Oct. 25, 2023, 9:02 p.m.