pathfindR 3.0.2

Minor Changes and Bug Fixes

• Fixed tests after pathfindR.data@2.2.0 release with change in structure of
  example_active_snws data

pathfindR 3.0.1

Minor Changes and Bug Fixes

• • Fixed signed integer overflow in the C++ active subnetwork search
    (java_string_hashcode) reported by gcc-UBSAN and clang-UBSAN on CRAN.
    Hash accumulation now uses defined unsigned-wrap arithmetic while preserving
    identical results. Also hardened JavaRandom::nextInt and java_cap_for
    against the same class of undefined behaviour.
• Removed unused component_labels utility function
• Fixed issue in create_term_gene_plot(): when no term_fill information is
  present in the input graph, the function should revert to default node colors

pathfindR 3.0.0

Major Changes

• Re-implemented the active subnetwork search (GR/SA/GA) in R and C++ (via
  Rcpp), removing the Java dependency. For GR and SA, results are numerically
  identical to the legacy JAR given the same seed and inputs.
• Renamed the exported function active_snw_search() to
  get_active_subnetworks() (its signature has also changed).
• Renamed the exported function filterActiveSnws() to
  filter_active_subnetworks().
• Renamed the utility function fetch_gene_set() to fetch_gene_sets().

Minor Changes and Bug Fixes

• Removed the package start-up message.
• Split term_gene_graph() into create_term_gene_graph() and
  create_term_gene_plot(): create_term_gene_graph() builds the igraph
  structure, while create_term_gene_plot() visualizes the graph from the
  information available in that igraph object.

pathfindR 2.7.0

Minor Changes and Bug Fixes

• Moved org.Hs.eg.db from "Imports" to "Suggests" per new CRAN policy. Relevant functions revert to default behaviour if the required package is not installed.

pathfindR 2.6.0

Minor Changes and Bug Fixes

• fixed missing argument issue in get_gene_sets_list(#230)
• refactored to introduce safe_get_content so that URL access issues are handled more gracefully

pathfindR 2.5.1

Minor Changes and Bug Fixes

• fixed NA values in kappa matrix generation that will cause error as part of the latest igraph update (#227)

pathfindR 2.5.0

Major Changes

• updated dependencies so that pathfindR depends on msigdbr (>= 24.1.0)
• added the new db_species argument to the get_mgsigdb_gsets() data generation function

Minor Changes and Bug Fixes

• fixed test assertions that will break as part of the latest ggplot2 update (#223)

pathfindR 2.4.2

Minor Changes and Bug Fixes

• fixed a bug in visualize_KEGG_diagram() where ggkegg was raising an error (#214)

pathfindR 2.4.1

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

pathfindR 2.4.0

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)