pathfindR (version 1.3.0)

cluster_graph_vis: Graph Visualization of Pathway Clustering

Description

Graph Visualization of Pathway Clustering

Usage

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

Arguments

clu_obj

clustering result (either a matrix obtained via `fuzzy_pw_clustering` or a vector obtained via `hierarchical_pw_clustering`)

kappa_mat

matrix of kappa statistics (output of `create_kappa_matrix`)

enrichment_res

data frame of pathway enrichment results

kappa_threshold

threshold for kappa statistics, defining strong relation (default = 0.35)

use_names

boolean to indicate whether to use pathway names instead of IDs (default = FALSE, i.e. use IDs)

Value

Plots a graph diagram of clustering results. Each node is a 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

# NOT RUN {
cluster_graph_vis(clu_obj, kappa_mat, enrichment_res)
# }