ipath

Quick Pathway Viz with iPath

From the landing page of iPath, choose one of four metabolomic maps: metabolism, secondary metabolites, antibiotics, and microbial metabolism.

Quick Start

We'll start here, which is the metabolic (or global) map that shows all KEGG metabolic pathways. For the control panel on the right of the page, in the Element Selection field, enter a list of compound IDs, the radius of their node when drawn, and their colour as a hex code, separated by spaces. e.g.:

C00417 W20 #ff0000
C00026 W20 #ff0000
R01900 W10 #33ff33

Here's a link to a website that helps you pick hex colour codes. On clicking Submit data, the entire map will be coloured in grey, except the 3 components that are drawn: two nodes on the TCA cycle (C00417 and C00026, highlighted in red, that is #ff0000), and one connecting line (R01900, a.k.a. "edge", which is actually a reaction, highlighted in bright green).

Advanced Options

Click on Show advanced options to reveal, well, more options:

• default edge width, default node radius and default opacity: properties of the nodes and connecting lines that are not highlighted.
• Keep original colors checkbox: option to keep original colours after submitting data.
• default colour: colour when the non-lighted nodes and edges get "grayed out".
• background colour: Background colour.
• Select whole pathways checkbox: This never appears to do anything, for some reason.
• Select whole modules checkbox: when checked, this will highlight all KEGG modules which each selected node resides in.
• Query reaction compounds checkbox: Functionality still unknown.
• Species filter: Select species-specific pathway map. Each species has a 3-letter species KEGG ID (e.g. homo sapiens is hsa, drosophila melanogaster is dme). Here's a link to the KEGG species catalogue; clickthrough on each of the species latin names to get their 3-letter KEGG species ID.

For a more comprehensive tutorial, here's a link to the video tutorials that iPath already provides.