run_pathfindR
into individual functions: active_snw_search
, enrichment_analyses
, summarize_enrichment_results
, annotate_pathway_DEGs
, visualize_pws
.pathmap
as visualize_hsa_KEGG
, updated the function to produce different visualizations for inputs with binary change values (ordered) and no change values (the input_processing
function, assigns a change value of 100 to all).visualize_pw_interactions
, which creates PNG files visualizing the interactions (in the selected PIN) of genes involved in the given pathways.create_kappa_matrix
, hierarchical_pw_clustering
, fuzzy_pw_clustering
and cluster_pathways
.cluster_graph_vis
for visualizing graph diagrams of clustering results.score_quan_thr
and sig_gene_thr
for run_pathfindR
were not being utilized.run_pathfindR
, added message at the end of run, reporting the number enriched pathways.run_pathfindR
now creates a variable org_dir
that is the “path/to/original/working/directory”. org_dir
is used in multiple functions to return to the original working directory if anything fails. This changes the previous behavior where if a function stopped with an error the directory was changed to “..”, i.e. the parent directory. This change was adapted so that the user is returned to the original working directory if they supply a recursive output folder (output_dir
, e.g. “./ALL_RESULTS/RESULT_A”).input_processing
, added the argument human_genes
to only perform alias symbol conversion when human gene symbols are provided. - Updated the Rmd files used to create the report HTML filesGO-All
, all annotations in the GO database (BP+MF+CC)pathfindR - An R Package for Pathway Enrichment Analysis Utilizing Active Subnetworks
to reflect the new functionalities.