cluster_enriched_terms | R Documentation |
Cluster Enriched Terms
cluster_enriched_terms(
enrichment_res,
method = "hierarchical",
plot_clusters_graph = TRUE,
use_description = FALSE,
use_active_snw_genes = FALSE,
...
)
enrichment_res |
data frame of pathfindR enrichment results. Must-have
columns are 'Term_Description' (if |
method |
Either 'hierarchical' or 'fuzzy'. Details of clustering are
provided in the corresponding functions |
plot_clusters_graph |
boolean value indicate whether or not to plot the graph diagram of clustering results (default = TRUE) |
use_description |
Boolean argument to indicate whether term descriptions
(in the 'Term_Description' column) should be used. (default = |
use_active_snw_genes |
boolean to indicate whether or not to use non-input active subnetwork genes in the calculation of kappa statistics (default = FALSE, i.e. only use affected genes) |
... |
additional arguments for |
a data frame of clustering results. For 'hierarchical', the cluster assignments (Cluster) and whether the term is representative of its cluster (Status) is added as columns. For 'fuzzy', terms that are in multiple clusters are provided for each cluster. The cluster assignments (Cluster) and whether the term is representative of its cluster (Status) is added as columns.
See hierarchical_term_clustering
for hierarchical
clustering of enriched terms.
See fuzzy_term_clustering
for fuzzy clustering of enriched terms.
See cluster_graph_vis
for graph visualization of clustering.
example_clustered <- cluster_enriched_terms(
example_pathfindR_output[1:3, ],
plot_clusters_graph = FALSE
)
example_clustered <- cluster_enriched_terms(
example_pathfindR_output[1:3, ],
method = 'fuzzy', plot_clusters_graph = FALSE
)
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