Changelog 1.5

pathfindR 1.5.02020-06-06

Major Changes

  • created separate package pathfindR.data for storing pathfindR data
  • added the function visualize_active_subnetworks() for visualizing graphs of active subnetworks
  • add the new vignette “Comparing Two pathfindR Results” that briefly describes how different pathfindR results can be compared
  • added the functions combine_pathfindR_results() and combined_results_graph() for comparison of 2 pathfindR results and term-gene graph of the combined results, respectively
  • added the function get_pin_file() for obtaining organism-specific PIN data (only from BioGRID for now)
  • added the function get_gene_sets_list() for obtaining organism-specific gene sets list from KEGG, Reactome and MSigDB
  • added the function term_gene_heatmap() to create heatmap visualizations of enriched terms and the involved input genes. Rows are enriched terms and columns are involved input genes. If genes_df is provided, colors of the tiles indicate the change values
  • added the function UpSet_plot() to create UpSet plots of enriched terms
  • added the human cell markers gene sets data cell_markers_gsets and cell_markers_descriptions

Minor Changes and Bug Fixes

  • fixed an issue regarding parallel::makeCluster() in run_pathfindR() (#45)
  • fixed save-related issue in download_kegg_png() (#37, @rix133)
  • added the output data RA_comparison_output of pathfindR results on another RA-related dataset (GSE84074)
  • in visualize_hsa_KEGG(), fixed the issue where >1 entrez ids were returned for a gene symbol (the first one is kept)
  • in visualize_hsa_KEGG(), implemented a tryCatch to avoid any issues when KEGGREST::color.pathway.by.objects() might fail (#28)
  • in visualize_hsa_KEGG(), now limiting the number of genes passes onto KEGGREST::color.pathway.by.objects() to < 60 (because the KEGG API now limits the number?)
  • changed default visualization in term_gene_heatmap() (i.e. when genes_df is not provided) to binary colored heatmap (by default, “green” and “red”, controlled by low and high) by up-/down- regulation status
  • update the vignette “pathfindR Analysis for non-Homo-sapiens organisms” to reflect new data generation functions get_pin_file() and get_gene_sets_list() and fixed a minor issue in the vignette (#46)

pathfindR 1.5.12020-09-20

Minor Changes and Bug Fixes