Cluster Enriched Terms
cluster_enriched_terms( enrichment_res, method = "hierarchical", plot_clusters_graph = TRUE, use_description = FALSE, use_active_snw_genes = FALSE, ... )
data frame of pathfindR enrichment results. Must-have
columns are "Term_Description" (if
use_description = TRUE) or "ID"
use_description = FALSE), "Down_regulated", and "Up_regulated".
use_active_snw_genes = TRUE, "non_Signif_Snw_Genes" must also be
boolean value indicate whether or not to plot the graph diagram of clustering results (default = TRUE)
Boolean argument to indicate whether term descriptions
(in the "Term_Description" column) should be used. (default =
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)
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.
example_clustered <- cluster_enriched_terms(RA_output[1:3, ], plot_clusters_graph = FALSE) #> The maximum average silhouette width was 0.06 for k = 2 #> example_clustered <- cluster_enriched_terms(RA_output[1:3, ], method = "fuzzy", plot_clusters_graph = FALSE)