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)

pathfindR 2.3.1

Minor Changes and Bug Fixes

• fixed a bug in the UpSet_plot() plot function regarding the interaction with ggupset package that was discovered in a reverse dependency check for ggplot2 3.5.0 (#189)
• fixed gene symbol case mismatch issue in score_terms() (#186)
• applied enhancement suggestion from #184 to enable scale fill manual for term_gene_graph()

pathfindR 2.3.0

Major Changes

• reverted removal of create_HTML_report() so run_pathfindR() once again generates HTML reports

pathfindR 2.2.0

Minor Changes and Bug Fixes

• added the disable_parallel argument in active_snw_enrichment_wrapper() to be able to disable parallel runs via foreach
• fixed the issue encountered on CentOS where forech wasn't loading pathfindR (#164)
• fixed a CRAN error due to a package documentation issue (#172)
• performed some refactoring and updated/improved all tests

pathfindR 2.1.0

Minor Changes

• removed create_HTML_report() so run_pathfindR() no longer generates a HTML report

pathfindR 2.0.1

Minor Changes

• added the dir_for_report argument in the internal function create_HTML_report() to fix test issues on CRAN

pathfindR 2.0.0

Major Changes

• updated the java active subnetwork search component and added the seedForRandom argument in active_snw_search()to ensure reproducibility. By default behavior, in run_pathfindR(), a seed is set for each iteration to produce reproducible results (#108)
• as the example input/output data were renamed for convenience in 'pathfindR.data' v2.0, 'pathfindR' now depends on pathfindR.data (>= 2.0)
• refactored/simplified run_pathfindR()
• visualization enriched term diagrams are now NOT part of run_pathfindR()
• default behavior of run_pathfindR() is now to run in a temporary directory. The user can still set output_dir to run in a specified directory and also produce HTML reports
• in hierarchical_term_clustering(), update the sequence of number of clusters for which silhouette width is calculated for choosing the optimal number of clusters. This should speed up the function for cases with a large number of enriched terms
• updated the relevant vignettes to reflect the implemented changes

Minor Changes

• fixed a minor issue in return_pin_path() where the PIN was not properly read (#157)

pathfindR 1.6.4

Minor Changes

• updated the alias selection function within input_processing() so that an alias that is not already present is selected
• updated the min-max scaling (controlled by scale_vals) in color_kegg_pathway(), the default is now scale_vals=TRUE
• updated the term_gene_heatmap() function so that legend title is shown and can be customized
• updated the term_gene_heatmap() function so that coloring is proper when no change values are provided in genes_df
• added the sort_terms_by_p argument to the term_gene_heatmap() function to enable sorting of terms by 'lowest_p'
• in visualization functions, made coloring of up-/down-regrulated genes consistent (#126)
• added the vertex.label.cex and vertex.size.scaling arguments to cluster_graph_vis()
• added the show_legend argument to visualize_term_interactions() to toggle the legend

pathfindR v1.6.3

Minor Changes

• Fixed coloring issue in color_kegg_pathway()
• In color_kegg_pathway() the default value for normalize_vals is now FALSE