This repository contains all scripts and Twig templates (HTML) used in a ChemInfo view for visualising a KEGG Pathway or Module. The user enters the Pathway or Module ID and, if validated correctly, the corresponding data are visualised. The work was moved into this repository as it was becoming somewhat complex to keep track of in the original repository, as well as departing somewhat from the purpose of the original repo.
The data used in the ChemInfo view are attached, thus the raw data are not found here. Collecting and extracting the data is completed according to the scripts here and here, and reformatting the data is completed using the scripts here and here.
Effectively, the queried data are objects, wherein the key is the KEGG Reaction, Module, or Pathway ID. Pathway IDs can be used to list corresponding Module or Reaction IDs, but in this case are used to list Reaction IDs only. Module IDs can be used to list Reaction IDs. Reaction IDs query the opposing compounds in the reaction equation, on the left- and right-hand sides of the reaction.
On loading the page, the attached data are loaded and the data objects are created in the API. The chart (simulation SVG) is then initialised and attached to the current window, such that it can be accessed from different ChemInfo cells and updated as necessary. The user then enters an ID into a text input and clicks a button to submit the string. The string is tested for suitable patterns, and, if suitable, is sent to the cell to run either the pathway or module visualisation, depending on the format of the ID. The attempt to update the simulation stops with an error if there is no matching ID found in the data. Otherwise, the data are queried to discover the appropriate reaction IDs, and the nodes and links arrays are generated, then created in the API. The cell to update the simulation then receives the data, and runs the update function.