color_kegg_pathway()
function using ggkegg
to create colored KEGG pathway ggplot objects (instead of using KEGGREST
to obtain the colored PNG files, which no longer works #169)visualize_hsa_KEGG
function to visualize_KEGG_diagram()
to reflect this is now able to handle KEGG pathway enrichment results from any organismvisualize_terms()
, visualize_term_interactions()
and visualize_KEGG_diagram()
functions so that they now return a list of ggplot objects (named by term ID)get_kegg_gsets()
function to also use ggkegg
for fetching genes per pathway datamagick
, KEGGgraph
and KEGGREST
get_biogrid_pin()
function so that it can now determine the latest version and download/process it from BioGRID (via setting release = "latest"
, which is now the default behavior)get_kegg_gsets()
which now returns KEGG IDs so that the user can convert the returned identifiers using a more appropriate tool (e.g. BioMart) should they wish