pathfindR.data
for storing pathfindR datavisualize_active_subnetworks()
for visualizing graphs of active subnetworkscombine_pathfindR_results()
and combined_results_graph()
for comparison of 2 pathfindR results and term-gene graph of the combined results, respectivelyget_pin_file()
for obtaining organism-specific PIN data (only from BioGRID for now)get_gene_sets_list()
for obtaining organism-specific gene sets list from KEGG, Reactome and MSigDBterm_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 valuesUpSet_plot()
to create UpSet plots of enriched termscell_markers_gsets
and cell_markers_descriptions
parallel::makeCluster()
in run_pathfindR()
(#45)download_kegg_png()
(#37, @rix133)RA_comparison_output
of pathfindR results on another RA-related dataset (GSE84074)visualize_hsa_KEGG()
, fixed the issue where >1 entrez ids were returned for a gene symbol (the first one is kept)visualize_hsa_KEGG()
, implemented a tryCatch to avoid any issues when KEGGREST::color.pathway.by.objects()
might fail (#28)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?)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 statusget_pin_file()
and get_gene_sets_list()
and fixed a minor issue in the vignette (#46)check_java_version()
where java version 14 could not be parsed (#49)combined_results_graph()
where gene nodes were not colored correctly (#55)