Creates a cytoscape pathway, where the reactions between compounds are also included in the nodes.
create_pathway_with_reactions(path, path.name, identified_cpds,
nodeNames="kegg", nodeTooltip=FALSE,
map.zoom=FALSE, map.layout="preset",
map.width=NULL, map.height=NULL)KEGGPathway object.
Name of the pathway.
Vector of kegg codes to color differently in the map.
How the nodes should be named. If "kegg", nodes are named with kegg codes. If "names", nodes are named with the common names.
Boolean value indicating if tooltips of nodes should appear when hovering with the mouse. Does not work for all environments (e.g. can be used in shiny apps).
Boolean value indicating if a zoom widget should appear or not. Does not work for all environments (e.g. can be used in shiny apps).
Layout of the map, available values are the ones of cytoscape ("breadthfirst", "preset", "cose", ...)
width of the map, in percentage (e.g. "80%"). May not work as expected in some environments.
Height of the map, in px (e.g. "500px"). May not work as expected in some environments.