Graph Visualization of Clustered Enriched Terms

cluster_graph_vis(
clu_obj,
kappa_mat,
enrichment_res,
kappa_threshold = 0.35,
use_description = FALSE
)

## Arguments

clu_obj clustering result (either a matrix obtained via hierarchical_term_clustering or fuzzy_term_clustering fuzzy_term_clustering or a vector obtained via hierarchical_term_clustering) matrix of kappa statistics (output of create_kappa_matrix) data frame of pathfindR enrichment results. Must-have columns are "Term_Description" (if use_description = TRUE) or "ID" (if use_description = FALSE), "Down_regulated", and "Up_regulated". If use_active_snw_genes = TRUE, "non_Signif_Snw_Genes" must also be provided. threshold for kappa statistics, defining strong relation (default = 0.35) Boolean argument to indicate whether term descriptions (in the "Term_Description" column) should be used. (default = FALSE)

## Value

Plots a graph diagram of clustering results. Each node is an enriched term from enrichment_res. Size of node corresponds to -log(lowest_p). Thickness of the edges between nodes correspond to the kappa statistic between the two terms. Color of each node corresponds to distinct clusters. For fuzzy clustering, if a term is in multiple clusters, multiple colors are utilized.

## Examples

if (FALSE) {
cluster_graph_vis(clu_obj, kappa_mat, enrichment_res)
}