run_pathfindRinto individual functions:
visualize_hsa_KEGG, updated the function to produce different visualizations for inputs with binary change values (ordered) and no change values (the
input_processingfunction, 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.
cluster_graph_visfor visualizing graph diagrams of clustering results.
run_pathfindRwere not being utilized.
run_pathfindR, added message at the end of run, reporting the number enriched pathways.
run_pathfindRnow creates a variable
org_dirthat is the “path/to/original/working/directory”.
org_diris 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_genesto only perform alias symbol conversion when human gene symbols are provided. - Updated the Rmd files used to create the report HTML files
GO-All, all annotations in the GO database (BP+MF+CC)
pathfindR - An R Package for Pathway Enrichment Analysis Utilizing Active Subnetworksto reflect the new functionalities.