As discovered through #169, the KEGGREST package (which pathfindR currently uses to generate hsa KEGG pathway diagrams) cannot obtain coloured KEGG pathway diagrams any more. As an alternative, this PR investigates potentially utilising ggkegg for this purpose. Additionally, this will allow us to:
instead of a static PNG file (current behaviour), we will be able to return ggplot objects that are further customisable
obtain KEGG pathway diagrams for any organism
remove dependencies on KEGGgraph, KEGGREST and magick
As discovered through #169, the
KEGGRESTpackage (whichpathfindRcurrently uses to generate hsa KEGG pathway diagrams) cannot obtain coloured KEGG pathway diagrams any more. As an alternative, this PR investigates potentially utilisingggkeggfor this purpose. Additionally, this will allow us to:ggplotobjects that are further customisableKEGGgraph,KEGGRESTandmagick