Changelog • KEGGemUP

KEGGemUP 0.99.1

Finalized some changes upon the Bioconductor package reviewing process
- render_kegg_graph() gains a graph_title parameter to override the displayed title
- fix in the vignette for correct rendering of the link to the RCy3 vignette
- added information on the fnd in the Authors section + formally acknowledged the contributions of the wet-lab collaborators (as ctb authors)

Better tooltip implementation
Highlighting of the nodes now takes care of graying out a bit more of elements that should indeed be not too much into the focus
Added export_kegg_graph() as a simple function to export the graphs to text files, for maximum compatibility with any framework (possibly even within Cytoscape)
Providing an example dataset already precomputed within the package to avoid additional dependency load; as a companion to this, added detailed information on how to create this in the inst/scripts folder
Finalized a full version of the vignette
Completed the configuration of the pkgdown documentation
Exporting also the cleanup_title_node() function to remove the title node in pathway graphs

Restructuring the API to use declarative function names, that possibly better convey the piece of functionality (create_kegg_graph() and render_kegg_graph() as the main workhorse)
The functions to retrieve the kgml files are now a bit more verbose if needed (retrieve_kgml() and retrieve_all_pathways())
Subsetting and highlighting KEGG graphs is now possible with subset_kegg_graph() and highlight_kegg_graph(), subsequently to be passed to render_kegg_graph()
The cache & download is handled in a more homogeneous manner, with display_cache_KEGGemUP() and reset_cache_KEGGemUP() to check and reset the info retrieved
Mapping continuous values from different DE-results like containers is handled by map_results_to_graph()

Essential functionality implemented, from kgml files all the way down to rendering interactively