create_pathway_with_reactions: Creates the pathway, with reactions included in the nodes.
In specmine: Metabolomics and Spectral Data Analysis and Mining

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)

`path`	KEGGPathway object.
`path.name`	Name of the pathway.
`identified_cpds`	Vector of kegg codes to color differently in the map.
`nodeNames`	How the nodes should be named. If "kegg", nodes are named with kegg codes. If "names", nodes are named with the common names.
`nodeTooltip`	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).
`map.zoom`	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).
`map.layout`	Layout of the map, available values are the ones of cytoscape ("breadthfirst", "preset", "cose", ...)
`map.width`	width of the map, in percentage (e.g. "80%"). May not work as expected in some environments.
`map.height`	Height of the map, in px (e.g. "500px"). May not work as expected in some environments.