mrtomrod / kegg-map-wizard

Downloads pathway maps from KEGG, creates Python obejcts, converts them into SVG, allows processing in modern browsers.

KeggMapWizard

Warning Using this tool may require a KEGG subscription!

This script downloads KEGG REST data, KEGG configs and KEGG PNGs and converts them into SVG maps which can be processed dynamically using modern browsers.

I included a simple JavaScript library that enables coloring the maps. It requires

• jQuery
• chroma.js to calculate color gradients
• html2canvas to render the SVGs as PNGs

Python

Creating the SVGs

Install the requirements. pip install poetry && poetry install

Set the environment variable KEGG_MAP_WIZARD_DATA to where you want data to be downloaded to.

export KEGG_MAP_WIZARD_DATA='/path/to/desired/download/location'

or in Python:

import os

os.environ['KEGG_MAP_WIZARD_DATA'] = '/path/to/desired/download/location'

In a Python 3.9 console, type:

from kegg_map_wizard import KeggMapWizard, KeggMap, KeggShape, KeggAnnotation, ColorMaker

kmw = KeggMapWizard(orgs=['ko', 'rn', 'ec'])  # merge ko, rn and ec annotations
kmw.download_maps()  # this will download all available KEGG maps
kmw.download_maps(map_ids=['00400'], reload=True)  # this will only download this specific KEGG map

# Create KeggMap object
kegg_map = kmw.create_map('00400')

# Create SVG
svg = kegg_map.svg()

# Save SVG
with open('/path/to/outfile.svg', 'w') as f:
    f.write(svg)

By default, all shapes are transparent. Below are some examples on how to apply colors:

def custom_color_function(shape: KeggShape):
    '''Color all shapes red'''
    return 'red'


def custom_color_function(shape: KeggShape):
    '''Color only shapes with the annotation K01623 red'''
    if ('K', 'K01623') in shape.annotations_dict:
        return 'red'
    else:
        return 'transparent'


def custom_color_function(shape: KeggShape):
    '''Color all shapes with 4 sequential colors (yellow, red, blue, green)'''
    shape.definition = ColorMaker.svg_gradient(
        colors=['yellow', 'red', 'blue', 'green'],
        id=shape.hash,
        x1=shape.bbox.x1,
        x2=shape.bbox.x2
    )
    return f'url(#{shape.hash})'


# Create svg using the custom_color_function
svg = kegg_map.svg(color_function=custom_color_function)

The last custom_color_function results in this:

The gradient is defined in shape.definition and looks like this:

<linearGradient id="{shape.hash}" gradientUnits="userSpaceOnUse" x1="{shape.bbox.x1}" x2="{shape.bbox.x2}">
    <stop offset="25%" stop-color="yellow"></stop><stop offset="25%" stop-color="red"></stop>
    <stop offset="50%" stop-color="red"></stop><stop offset="50%" stop-color="blue"></stop>
    <stop offset="75%" stop-color="blue"></stop><stop offset="75%" stop-color="green"></stop>
</linearGradient>

Testing and colouring SVGs

To test the maps, run a simple http server in the kegg_map_wizard: python -m http.server 8000

Then open http://localhost:8000/kegg_map_wizard/html/map_tester.html

JavaScript

Shapes can not just be colored via Python, but also via JavaScript in the web browser.

For an example, see how this library is used in OpenGenomeBrowser .

Required SVG format

The svg should have a title attribute. Example:

<svg
        title='Phenylalanine, tyrosine and tryptophan biosynthesis'
        version='1.1' baseProfile='full' xmlns='http://www.w3.org/2000/svg' xmlns:xlink='http://www.w3.org/1999/xlink'
        <!-- other attributes -->
        >

Each enzyme in the SVG needs to belong to the class shape and have the data-annotations-attribute. Example:

<circle cx='978' cy='930' r='4' fill='transparent'  <!-- Must not be circle, can be any other SVG element -->
        title='C00296 (Quinate)'  <!-- will tooltip -->
        class='shape compound'  <!-- only class 'shape' is required -->
        data-annotations='[{"description": "L-Ectoine", "name": "C06231", "type": "KEGG Compound"}]'>  <!-- see below -->
        />

The data-annotations-attribute tells the KeggMapWizard library which annotations are behind the shape.

Example:

[
  {
    "description": "L-Ectoine",
    "name": "C06231",
    "type": "KEGG Compound"
  }
]

How access the properties using JavaScript/jQuery

append a click event listener to all shapes:

$('.shape').click(function (event) {
    showMapMenu(event, this)
})

loop over all shapes:

$(".shape").each(function () {
    // do something
    console.log($(this).attr('title'))  // or 'data-original-title'
})

read data-annotations into a variable, loop over annotations, save the changes back into data-annotations:

let annotations = $(shape).data('annotations')  // read
annotations.forEach(function (annotation, index) {
    // do something
    console.log(annotation['name'])
})
$(shape).data('annotations', annotations)  // save changes

How to use PathwaySvgLib functions

highlight specific annotations:

highlightBinary(
    color = "green",
    annotations_to_highlight = ["R01518", "K15778", "K22473"]
)

color using continuous numbers:

highlightContinuous(
    svg = document.getElementById('custom-kegg').firstChild,
    annotation_to_number = {R01518: 0, K15778: 0.5, K22473: 1},
    colors = ['yellow', 'red']
)

color organisms with gradient:

highlightOrganisms(
    svg = document.getElementById('some-svg'),
    organisms = {
        "Organism 1": ["R01518", "K15778", "K22473"],
        "Organism 2": ["K02446", "R00959", "C01172"],
        "Organism 3": ["R01518", "K00129", "EC:2.7.1.147"]
    },
    colors = ['yellow', 'red']
)

color groups of organisms with gradient:

highlightGroupsOfOrganisms(
    svg = document.getElementById('some-svg'),
    groupsOfOrganisms = {
        Grp1: {
            "Organism 1": ["R01518", "K15778", "K22473"],
            "Organism 2": ["K02446", "R00959", "C01172"],
            "Organism 3": ["R01518", "K00129", "EC:2.7.1.147"]
        },
        Grp2: {
            "Organism 4": ["R01518", "K15778", "K22473"],
            "Organism 5": ["K02446", "R00959", "C01172"]
        },
    }
)

The enzyme boxes will be separated into as many areas as there are groups. Group 1 organisms color the leftmost area, group 2 the second from the left, etc.

save map as PNG

saveDivAsPng('id-of-svg')

kegg-map-wizard's Issues

Add KEGG modules?

Create maps using matplotlib/seaborm like this:

Each shape has to incorporate more logic, though, as defined by the KEGG modules.

Idea from u/Freevini

Use recent CSS feature color-mix()?

Link to Mozilla Web Docs.

Probably not supported by most SVG readers...

Could reduce dependency on chroma.js.