Heat map is useful tool to visualise multi parameter not only biology, but also chemoinformatics.
I often use spot-fire or R to make it.
Last week I found cool javascript library “InCHlib(Interactive Cluster Heatmap library)”.
There is good document in this link http://openscreen.cz/software/inchlib/home/ .
I make simple test to use the library.
At first, I wrote app.py in my folder. (Use flask.)
from flask import Flask
from flask_bootstrap import Bootstrap
from flask import render_template
def create_app():
app = Flask( __name__ )
Bootstrap( app )
return app
app = create_app()
@app.route("/")
def root():
return render_template("sample.html")
if __name__=="__main__":
app.run(debug = True)
I set three javascript librarys in static/js folder
kinetic-v5.1.0.min.js, jquery-2.0.3.min.js, inchlib-1.1.0.js
First, I make dataset using rdkit, and pandas.
Sample data is CDK2 inh. download form chembldb.
To make sampledata, I made two dataset, firstdata.csv(mol_id, and some descriptors), metadata.csv(mol_id and biological data).
iwatobipen$ head -n 5 firstdata.csv CMPD_CHEMBLID,MOLWT,LOGP,RING,HDN,HACC,NRotB CHEMBL573578,331.4230000000001,3.9075000000000024,4,1,5,2 CHEMBL270724,463.745,4.8344000000000005,1,1,1,2 CHEMBL75680,267.332,3.6731000000000025,3,2,3,4 CHEMBL281948,467.4810000000003,3.655100000000002,8,2,7,1 iwatobipen$ head -n 5 metadf.csv CMPD_CHEMBLID,STANDARD_VALUE CHEMBL573578,57 CHEMBL270724,67 CHEMBL75680,18 CHEMBL281948,0
Then, make data using inchlib_clust.py.
“-dh and -mh” option mean that use header(column names) in csv files.
python inchlib_clust.py firstdata.csv -m metadata.csv -dh -mh -o cdk2.json
Now I got cdk2.json file that contains the cluster heatmap in the InCHlib input format.
Next, write html template.
1.Base template using bootstrap.
{% extends "bootstrap/base.html" %}
{% block title %}{% endblock %}
{% block navbar %}
<nav class="navbar navbar-inverse navbar-fixed-top" role="navigation">
<!-- -->
<div class="container-fluid">
<!-- Brand and toggle get grouped for better mobile display -->
<div class="navbar-header">
<button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#bs-example-navbar-collapse-1">
<span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<a class="navbar-brand" href="#">sample</a>
</div>
<!-- Collect the nav links, forms, and other content for toggling -->
<div class="collapse navbar-collapse" id="bs-example-navbar-collapse-1">
<ul class="nav navbar-nav">
<li class="active"><a href="/">Top</a></li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown">Dropdown <span class="caret"></span></a>
<ul class="dropdown-menu" role="menu">
<li><a href="#">hoge</a></li>
<li class="divider"></li>
<li><a href="#">Separated link</a></li>
<li class="divider"></li>
<li><a href="#">One more separated link</a></li>
</ul>
</li>
</ul>
<form class="navbar-form navbar-left" role="search">
<div class="form-group">
<input type="text" class="form-control" placeholder="Search">
</div>
<button type="submit" class="btn btn-default">Submit</button>
</form>
<ul class="nav navbar-nav navbar-right">
<li><a href="#">Link</a></li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown">Dropdown <span class="caret"></span></a>
<ul class="dropdown-menu" role="menu">
<li><a href="#">Action</a></li>
<li><a href="#">Another action</a></li>
<li><a href="#">Something else here</a></li>
<li class="divider"></li>
<li><a href="#">Separated link</a></li>
</ul>
</li>
</ul>
</div><!-- /.navbar-collapse -->
</div><!-- /.container-fluid -->
</nav>
{% endblock %}
{% block content %}
{% endblock %}
2.sample page.
This sample page shows heatmap and structure depends on mouse position.
{% extends "templ.html" %}
{% block title %} InCHlib {% endblock %}
{% block styles %}
{{super()}}
<style type="text/css">
#molecule{
position: absolute;
height: 305px;
width: 220px;
z-index: 100;
border: solid #D2D2D2 1px;
border-radius: 10px;
display: none;
background-color: white;
}
#molecule_img{
margin-left: auto;
margin-right: auto;
display: block;
width: 95%;
background-color: white;
border-radius: 10px;
}
</style>
{% endblock %}
{% block scripts %}
{{ super() }}
<script type=text/javascript src="{{ url_for('static', filename='js/jquery-2.0.3.min.js')}}"></script>
<script type=text/javascript src="{{ url_for('static', filename='js/kinetic-v5.1.0.min.js')}}"></script>
<script type=text/javascript src="{{ url_for('static', filename='js/inchlib-1.1.0.js')}}"></script>
<script>
// load JSON
$(document).ready(function() { //run when the whole page is loaded
window.inchlib = new InCHlib({ //instantiate InCHlib
target: "inchlib", //ID of a target HTML element
metadata: true, //turn on the metadata
column_metadata: true, //turn on the column metadata
max_height: 1200, //set maximum height of visualization in pixels
width: 600, //set width of visualization in pixels
heatmap_colors: "Greens", //set color scale for clustered data
metadata_colors: "Reds", //set color scale for metadata
});
inchlib.read_data_from_file("{{ url_for('static', filename='demodata/cdk2.json')}}"); //read input json file
inchlib.draw(); //draw cluster heatmap
var molecule_url = "{{ url_for('static', filename='img/')}}";
var target_element = $("#inchlib");
var offset = target_element.offset();
var x_pos = offset.left + inchlib.settings.width - 80;;
var max_y = offset.top+150;
var img_element = $("#molecule_img");
var mol_element = $("#molecule").css({"left" : x_pos});
var mol_id_element = $("mol_id");
var floating_mol = $("#floating_mol");
bind_dendrogram_events();
function show_molecule(mol_id, evt){
var filepath = molecule_url + mol_id + ".png";
var y = evt.evt.pageY-300;
if(y < max_y){
y = max_y;
}
mol_element.css({"top": y, "border-width": "1px"});
img_element.attr("src", filepath);
mol_id_element.text(mol_id);
//mol_link.attr("href", chembl_url+mol_id);
mol_element.show();
}
function hide_molecule(ids, evt){
mol_element.hide();
}
function fix_molecule(){
floating_mol.hide();
inchlib.events.row_onmouseover = function(){};
inchlib.events.heatmap_onmouseout = function(){
floating_mol.hide();
};
}
function bind_dendrogram_events(){
inchlib.events.row_onmouseover = function(ids, evt){
show_molecule(ids, evt);
};
inchlib.events.heatmap_onmouseout = function(evt){
hide_molecule(evt);
floating_mol.hide();
};
inchlib.events.row_onclick = function(ids, evt){
show_molecule(ids[0], evt);
fix_molecule(ids[0]);
current_mol = ids[0];
inchlib.highlight_rows(ids);
mol_element.css({"border-width": "2px"});
inchlib.unhighlight_cluster();
};
inchlib.events.dendrogram_node_highlight = function(object_ids, evt){
var i;
for(i = 0; i<object_ids.length; i++){
if(object_ids[i] == current_mol){
return;
}
}
inchlib.highlight_rows([]);
}
inchlib.events.empty_space_onclick = function(){
hide_molecule();
inchlib.highlight_rows([]);
bind_dendrogram_events();
}
}
$(document).click(function(evt){
if(evt.target.localName != "img" && evt.target.localName != "canvas" && evt.target.localName != "a"){
hide_molecule();
bind_dendrogram_events();
}
});
});
</script>
{% endblock %}
{% block content %}
<div class="container-fluid">
<div class="row">
<h1>InCHlib test</h1></br>
<div class="col-md-12" style='background-color: lightblue; height: 1200px'>
<div id="inchlib"></div>
<div id="molecule">
<h1></h1>
<img src="" id="molecule_img" style=""></img>
</div>
</div>
</div>
</div>
{% endblock %}
Finally run app and access 127.0.0.1:5000/ .
In summary, InCHlib is very cool tools to visualise molecular structures and biological activity or another data in web.
I uploaded sample to github.
https://github.com/iwatobipen/inchlib-test
Advertisements
