cmp_make_plot: Make plots for comparing clustering methods

View source: R/compare_methods.R

cmp_make_plotR Documentation

Make plots for comparing clustering methods

Description

Make plots for comparing clustering methods

Usage

cmp_make_plot(mat, clt, plot_type = c("mixed", "heatmap"), nrow = 3)

Arguments

mat

A similarity matrix.

clt

A list of clusterings from cmp_make_clusters.

plot_type

What type of plots to make. See Details.

nrow

Number of rows of the layout when plot_type is set to heatmap.

Details

If plot_type is the default value mixed, a figure with three panels generated:

  • A heatmap of the similarity matrix with different classifications as row annotations.

  • A heatmap of the pair-wise concordance of the classifications of every two clustering methods.

  • Barplots of the difference scores for each method (calculated by difference_score), the number of clusters (total clusters and the clusters with size >= 5) and the mean similarity of the terms that are in the same clusters.

If plot_type is heatmap. There are heatmaps for the similarity matrix under clusterings from different methods. The last panel is a table with the number of clusters under different clusterings.

Value

No value is returned.

Examples

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

## End(Not run)

jokergoo/simplifyEnrichment documentation built on Nov. 3, 2023, 2:57 p.m.