Visualizing biological graphs in Cytoscape.js

G R A P H S I N C Y T O S C A P E . J S
V I S U A L I Z I N G B I O L O G I C A L
Ben Keller 
linkedin.com/in/bjkeller
Seattle/Bellevue Graphs - Data, Processing, Algorithms Meetup 
6 May 2014

B I O L O G I C A L G R A P H S

( S I G N A L I N G ) PAT H WAY S
N AT U R E N E U R O S C I E N C E 1 3 , 6 – 7 ( 2 0 1 0 ) D O I : 1 0 . 1 0 3 8 / N N 0 1 1 0 - 6

P R O T E I N - P R O T E I N I N T E R A C T I O N S
A B
http://www.stats.ox.ac.uk/~hamer/research.html

P R O T E I N - P R O T E I N I N T E R A C T I O N S
A B

E X A M P L E P P I G R A P H
ANK3
CABP1
CACNA
2D4
CACNB
3
GNB1
PCBD1
RIMS1
PPM1A
PRKAC
A
RYR2
SRI
CACNA
1C
FAS
FADD
CNTN1
CRKL
HOOK1
KCNC1
KCNC2
SMAD3
SMAD2
PIK3R1
SPTBN4
SCN1B
SCNN1
B
SCN2A

AT T R I B U T E S
Tell us something about gene/protein:
• Where it occurs
• What it does
• What processes it contributes to
• What diseases it is implicated in
Allow us to ask
• do these genes belong together?
• do they work together?

P R O T E I N - A N N O TAT I O N G R A P H
MeSH: Calcium
GO BP: Metal Ion Transport
GO MF: Gated Channel Activity
GO MF: Cation Channel Activity
OR
MeSH Ion Channel Gating
MeSH: Phosphorylation
MeSH: Intercellular Signaling
Peptides and Proteins
MeSH: Nerve
Tissue Proteins
CRKL
ANK3
CABP1
CACNA
2D4
CACNB
3
GNB1
PCBD1
RIMS1
PPM1A
PRKAC
A
RYR2
SRI
CACNA
1C
FAS
FADD
CNTN1
HOOK1
KCNC1
KCNC2
SMAD3
SMAD2
PIK3R1
SPTBN4
SCN1B
SCNN1
B
SCN2A
None

C O N C E P T G R A P H
MeSH: Calcium
OR
MeSH: Nerve
Tissue Proteins
CRKL
ANK3
CABP1
CACNA
2D4
CACNB
3
GNB1
PCBD1
RIMS1
PPM1A
PRKAC
A
RYR2
SRI
CACNA
1C
FAS
FADD
CNTN1
HOOK1
KCNC1
KCNC2
SMAD3
SMAD2
PIK3R1
SPTBN4
SCN1B
SCNN1
B
SCN2A
None
MeSH: Calcium
OR
MeSH: Nerve
Tissue Proteins

MeSH: Calcium
GO MF: Voltage-Gated Ion Channel Activity
MeSH: Signal Transduction
MeSH: Intercellular Signaling Peptides and Proteins
MeSH: Rats
MeSH: Nerve Tissue Proteins
CRKL
ANK3
CABP1
CACNA
2D4
CACNB
3
GNB1
PCBD1
RIMS1
PPM1A
PRKAC
A
RYR2
SRI
CACNA
1C
FAS
FADD
CNTN1
HOOK1
KCNC1
KCNC2
SMAD3
SMAD2
PIK3R1
SPTBN4
SCN1B
SCNN1
B
SCN2A

MeSH: Calcium
OR
MeSH: Nerve
Tissue Proteins
CRKL
ANK3
CABP1
CACNA
2D4
CACNB
3
GNB1
PCBD1
RIMS1
PPM1A
PRKAC
A
RYR2
SRI
CACNA
1C
FAS FADD
CNTN1
HOOK1
KCNC1
KCNC2
SMAD3
SMAD2
PIK3R1
SPTBN4
SCN1B
SCNN1
B
SCN2A

( J S B I N ) H T M L
<!DOCTYPE html>
<html>
<head>
<meta charset="utf-8">
<title>Meetup Cytoscape.js Lab</title>
<script src="http://ajax.googleapis.com/ajax/libs/jquery/1/jquery.min.js"></script>
<script src="http://cytoscape.github.io/cytoscape.js/api/cytoscape.js-latest/cytoscape.min.js"></script>
</head>
<body>
<div id="cy" style="height:90%;width:90%;position:absolute;left:0;top:0;"></div>
</body>
</html>
• jQuery
• cytoscape.js
• (your script)
container for graph

J S F I L E
$(document).ready(function(){
//cytoscape code goes here
});

C Y T O S C A P E S E S S I O N
var cy = cytoscape({
container: document.getElementById('cy'),
ready: function() {}
});

G R A P H
var graphelements = {
nodes: [
{ data: { id: 'n1', name: ‘A' } },
{ data: { id: 'n2', name: ‘B' } },
{ data: { id: 'n3', name: ‘C' } },
{ data: { id: 'n4', name: ‘D' } }
],
edges: [
{ data: { id: 'e1', source: 'n1', target: 'n2' } },
{ data: { id: 'e2', source: 'n3', target: 'n2' } },
{ data: { id: 'e3', source: 'n4', target: 'n2' } }
]
};

A D D : S H O W N O D E L A B E L O N H O V E R
cy.on('mouseover','node',function(evt) {
var node = evt.cyTarget;
node.css('content','data(name)');
});
cy.on('mouseout','node',function(evt){
var node = evt.cyTarget;
node.css('*','');
});
(add after session definition)http://jsbin.com/reqeg/12/edit

A D D : S E T U P F O R S T Y L E S
var nodestyle = {};
var edgestyle = {};
!
var stylesheet = cytoscape.stylesheet(). 
selector("node").css(nodestyle).
selector(“edge").css(edgestyle);
!
var cy = cytoscape({
container: document.getElementById('cy'),
style: stylesheet,
ready: function() {}
});
http://jsbin.com/reqeg/11/edit

A D D : S E T N O D E S T Y L E
var nodestyle = {
'font-size': '12pt',
'min-zoomed-font-size': ‘9pt',
'text-halign': 'center',
'text-valign': 'center',
'color': 'white'
};

A D D : M A P P I N G AT T R I B U T E S ( 1 )
var nodestyle = {
'font-size': '12pt',
'min-zoomed-font-size': '9pt',
'text-valign': 'center',
'text-halign': 'center',
'color': 'white',
'width': 'mapData(degree,0,5,20,80)',
'height': 'mapData(degree,0,5,20,80)'
};

A D D : M A P P I N G AT T R I B U T E S ( 2 )
var degmap = {};
var nodes = cy.nodes();
for (var i = 0; i < nodes.length; i++) {
degmap[nodes[i].id()] = { degree: nodes[i].degree() };
}
cy.batchData(degmap);

L AY O U T S
var layoutopts = {
name: 'breadthfirst',
roots: ['n1','n26']
};
cy.layout(layoutopts);
• random
• preset
• grid
• circle
• concentric
• breadthfirst
• arbor *
• cose
• null (for algorithms)

A R B O R ( F O R C E - D I R E C T E D )
<script src="../node_modules/cytoscape/lib/arbor.js"></script>
<script src="../node_modules/cytoscape/dist/cytoscape.min.js"></script>

http://cytoscape.github.io/cytoscape.js/
http://bumbu.github.io/cytoscape.js/debug/

Visualizing biological graphs in Cytoscape.js

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