cmp_make_plot {simplifyEnrichment} | R 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)

[Package simplifyEnrichment version 1.2.0 Index]