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)

Major Changes

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

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


Minor Changes

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