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

pathfindR v1.6.2

Major Changes

• fixed an issue in get_kegg_gsets() where empty result was returned for some organisms due to an error in parsing (#72)

Minor changes and bug fixes

• added repel = TRUE in term_gene_graph() and combined_results_graph() for better visualization of labels
• fixed minor issue in enrichment_chart() (#75)
• fixed minor issue in visualize_term_interactions()
• fixed issue in get_biogrid_pin() where the download method was set to wget (now set to auto, per #83)
• updated to using tab3 format for get_biogrid_pin() (if tab3 is available for the chosen release, otherwise tab2 format is used)
• updated the default version of PIN obtained by get_biogrid_pin() to '4.4.200'
• in get_kegg_gsets(), improved parsing of KEGG term descriptions so that no description is duplicated (#87)
• in score_terms(), if using descriptions, the ID is now appended for (any) duplicated term descriptions (#87)
• in obtain_colored_url(), swapped bg_color with fg_color due to an issue with KEGGREST
• added legend to term_gene_heatmap() (#95)
• in get_biogrid_pin(), the "download.file.method" from global options is used
• combined_results_graph() raises an error if there are no common terms in the combined data frame

---

pathfindR v1.6.1

Major Changes

• In run_pathfindR(), the default iterations was set back to 10 (the default for all other v1.x)

pathfindR v1.6.0

Major Changes

• In run_pathfindR(), as "GR" (the default active subnetwork search method) provides nearly identical results in each iteration, the default iterations is set to 1
• added the column 'support' (the proportion of active subnetworks leading to enrichment over all subnetworks) in the output
• updated the download URL in get_biogrid_pin() as BioGRID updated the URL for download

Minor changes and bug fixes

• changed old argument in the "Step-by-Step Execution of the pathfindR Enrichment Workflow" vignette
• fixed an issue in visualize_term_interactions() where the file name was too long, it was causing an error on Windows. Limited to 100 characters (#58)

pathfindR 1.6.0.9005

Major Changes

• In run_pathfindR(), as "GR" (the default active subnetwork search method) provides nearly identical results in each iteration, the default iterations is set to 1
• added the column 'support' (the proportion of active subnetworks leading to enrichment over all subnetworks) in the output

Minor changes and bug fixes

• changed old argument in the "Step-by-Step Execution of the pathfindR Enrichment Workflow" vignette
• fixed an issue in visualize_term_interactions() where the file name was too long, it was causing an error on Windows. Limited to 100 characters (#58)

pathfindR v1.5.1

Minor changes and bug fixes

• Fixed issue in check_java_version() where java version 14 could not be parsed (#49)
• Fixed issue in combined_results_graph() where gene nodes were not colored correctly (#55)

pathfindR 1.5.1.9001

• Fixed issue in check_java_version() where java version 14 could not be parsed (#49)
• Fixed issue in combined_results_graph() where gene nodes were not colored correctly (#55)

pathfindR v1.5.0

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 1.5.0.9010

• minor changes before v1.5.0 release

pathfindR 1.5.0.9009

• implemented workaround for the makePSOCKcluster update issue in run_pathfindR()
• implemented a fix for layout issue in combined_results_graph()