cmp_make_plot.Rd
Make plots for comparing clustering methods
cmp_make_plot(mat, clt, plot_type = c("mixed", "heatmap"), nrow = 3)
A similarity matrix.
A list of clusterings from cmp_make_clusters
.
What type of plots to make. See Details.
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.
# \dontrun{
mat = readRDS(system.file("extdata", "random_GO_BP_sim_mat.rds",
package = "simplifyEnrichment"))
clt = cmp_make_clusters(mat)
#> Cluster 500 terms by 'binary_cut'...
#> 19 clusters, used 1.084646 secs.
#> Cluster 500 terms by 'kmeans'...
#> 15 clusters, used 3.048331 secs.
#> Cluster 500 terms by 'pam'...
#> 5 clusters, used 19.44946 secs.
#> Cluster 500 terms by 'dynamicTreeCut'...
#> 60 clusters, used 0.140182 secs.
#> Cluster 500 terms by 'apcluster'...
#> 41 clusters, used 0.7691259 secs.
#> Cluster 500 terms by 'hdbscan'...
#> 14 clusters, used 0.1722541 secs.
#> Cluster 500 terms by 'fast_greedy'...
#> 6 clusters, used 0.1023328 secs.
#> Cluster 500 terms by 'louvain'...
#> 6 clusters, used 0.08096695 secs.
#> Cluster 500 terms by 'walktrap'...
#> 6 clusters, used 0.2634952 secs.
#> Cluster 500 terms by 'MCL'...
#> 6 clusters, used 2.234812 secs.
cmp_make_plot(mat, clt)
cmp_make_plot(mat, clt, plot_type = "heatmap")
# }