Major Changes

  • Separated the steps of the function run_pathfindR into individual functions: active_snw_search, enrichment_analyses, summarize_enrichment_results, annotate_pathway_DEGs, visualize_pws.
  • renamed the function 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).
  • Created new the visualization function visualize_pw_interactions, which creates PNG files visualizing the interactions (in the selected PIN) of genes involved in the given pathways.
  • Added new vignette, describing the step-by-step execution of the pathfindR workflow
  • Changed clustering metric to kappa statistic, created the new clustering related functions create_kappa_matrix, hierarchical_pw_clustering, fuzzy_pw_clustering and cluster_pathways.
  • Implemented the new function cluster_graph_vis for visualizing graph diagrams of clustering results.

Minor changes and bug fixes

  • Fixed the bug where the arguments score_quan_thr and sig_gene_thr for run_pathfindR were not being utilized.
  • in run_pathfindR, added message at the end of run, reporting the number enriched pathways.
  • the function 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”).
  • in 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 files
  • Added the data for GO-All, all annotations in the GO database (BP+MF+CC)
  • Updated the vignette pathfindR - An R Package for Pathway Enrichment Analysis Utilizing Active Subnetworks to reflect the new functionalities.