Major Changes

  • implemented a new color_kegg_pathway() function using ggkegg to create colored KEGG pathway ggplot objects (instead of using KEGGREST to obtain the colored PNG files, which no longer works #169)
  • renamed the visualize_hsa_KEGG function to visualize_KEGG_diagram() to reflect this is now able to handle KEGG pathway enrichment results from any organism
  • updated the visualize_terms(), visualize_term_interactions() and visualize_KEGG_diagram() functions so that they now return a list of ggplot objects (named by term ID)
  • updated the get_kegg_gsets() function to also use ggkegg for fetching genes per pathway data
  • removed unneeded dependencies: magick, KEGGgraph and KEGGREST

Minor Changes and Bug Fixes

  • updated the get_biogrid_pin() function so that it can now determine the latest version and download/process it from BioGRID (via setting release = "latest", which is now the default behavior)

Minor Changes and Bug Fixes

  • fixed a bug regarding KEGG gene set fetching: removed the conversion functionality in get_kegg_gsets() which now returns KEGG IDs so that the user can convert the returned identifiers using a more appropriate tool (e.g. BioMart) should they wish