Version 1.6 • pathfindR

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

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)

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

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

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

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-regulated 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

Changelog 1.6