cmp_make_plot: Make plots for comparing clustering methods
In simplifyEnrichment: Simplify Functional Enrichment Results

Description Usage Arguments Details Value Examples

Make plots for comparing clustering methods

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

`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`.

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.

No value is returned.

## 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)