Cytoscape Layouts
The layout parameter of cyto.Cytoscape takes as argument a
dictionary specifying how the nodes should be positioned on the screen.
Every graph requires this dictionary with a value specified for the
name key. It represents a built-in display method, which is one of the
following:
- preset
- random
- grid
- circle
- concentric
- breadthfirst
- cose
All those layouts, along with their options, are described in the
official Cytoscape documentation.
There, you can find the exact keys accepted by your dictionary, enabling
advanced fine-tuning (demonstrated below).
If preset is given, the positions will be rendered based on the positions
specified in the elements. Otherwise, the positions will be computed by
Cytoscape.js behind the scene, based on the given items of the layout
dictionary. Let’s start with an example of declaring a graph with a preset
layout:
using Dash, DashCytoscape
app = dash()
nodes = [
Dict(
"data" => Dict("id" => short, "label" => label),
"position" => Dict("x" => 20*lat, "y" => -20*long)
)
for (short, label, long, lat) in (
("la", "Los Angeles", 34.03, -118.25),
("nyc", "New York", 40.71, -74),
("to", "Toronto", 43.65, -79.38),
("mtl", "Montreal", 45.50, -73.57),
("van", "Vancouver", 49.28, -123.12),
("chi", "Chicago", 41.88, -87.63),
("bos", "Boston", 42.36, -71.06),
("hou", "Houston", 29.76, -95.37)
)
]
edges = [
Dict("data" => Dict("source" => source, "target" => target))
for (source, target) in (
("van", "la"),
("la", "chi"),
("hou", "chi"),
("to", "mtl"),
("mtl", "bos"),
("nyc", "bos"),
("to", "hou"),
("to", "nyc"),
("la", "nyc"),
("nyc", "bos")
)
]
elements = vcat(nodes, edges)
app.layout = cyto_cytoscape(
id="cytoscape-layout-1",
elements=elements,
style=Dict("width" => "100%", "height" => "350px"),
layout=Dict(
"name" => "preset"
)
)
run_server(app, "0.0.0.0", debug=true)
Here, we provided toy elements using geographically positioned nodes. If
you’d like to reproduce this example by yourself, check out the code
below.
View Elements Declaration
View Elements Declaration
nodes = [
Dict(
"data" => Dict("id" => short, "label" => label),
"position" => Dict("x" => 20*lat, "y" => -20*long)
)
for (short, label, long, lat) in (
("la", "Los Angeles", 34.03, -118.25),
("nyc", "New York", 40.71, -74),
("to", "Toronto", 43.65, -79.38),
("mtl", "Montreal", 45.50, -73.57),
("van", "Vancouver", 49.28, -123.12),
("chi", "Chicago", 41.88, -87.63),
("bos", "Boston", 42.36, -71.06),
("hou", "Houston", 29.76, -95.37)
)
]
edges = [
Dict("data" => Dict("source" => source, "target" => target))
for (source, target) in (
("van", "la"),
("la", "chi"),
("hou", "chi"),
("to", "mtl"),
("mtl", "bos"),
("nyc", "bos"),
("to", "hou"),
("to", "nyc"),
("la", "nyc"),
("nyc", "bos")
)
]
elements = vcat(nodes, edges)
Display Methods
In most cases, the position of the nodes will not be given. In these
cases, one of the built-in methods can be used. Let’s see what happens
when the value of name is set to 'circle' or 'grid'
using Dash, DashCytoscape
app = dash()
nodes = [
Dict(
"data" => Dict("id" => short, "label" => label),
"position" => Dict("x" => 20*lat, "y" => -20*long)
)
for (short, label, long, lat) in (
("la", "Los Angeles", 34.03, -118.25),
("nyc", "New York", 40.71, -74),
("to", "Toronto", 43.65, -79.38),
("mtl", "Montreal", 45.50, -73.57),
("van", "Vancouver", 49.28, -123.12),
("chi", "Chicago", 41.88, -87.63),
("bos", "Boston", 42.36, -71.06),
("hou", "Houston", 29.76, -95.37)
)
]
edges = [
Dict("data" => Dict("source" => source, "target" => target))
for (source, target) in (
("van", "la"),
("la", "chi"),
("hou", "chi"),
("to", "mtl"),
("mtl", "bos"),
("nyc", "bos"),
("to", "hou"),
("to", "nyc"),
("la", "nyc"),
("nyc", "bos")
)
]
elements = vcat(nodes, edges)
app.layout = cyto_cytoscape(
id="cytoscape-layout-2",
elements=elements,
style=Dict("width" => "100%", "height" => "350px"),
layout=Dict(
"name" => "circle"
)
)
run_server(app, "0.0.0.0", debug=true)
using Dash, DashCytoscape
app = dash()
nodes = [
Dict(
"data" => Dict("id" => short, "label" => label),
"position" => Dict("x" => 20*lat, "y" => -20*long)
)
for (short, label, long, lat) in (
("la", "Los Angeles", 34.03, -118.25),
("nyc", "New York", 40.71, -74),
("to", "Toronto", 43.65, -79.38),
("mtl", "Montreal", 45.50, -73.57),
("van", "Vancouver", 49.28, -123.12),
("chi", "Chicago", 41.88, -87.63),
("bos", "Boston", 42.36, -71.06),
("hou", "Houston", 29.76, -95.37)
)
]
edges = [
Dict("data" => Dict("source" => source, "target" => target))
for (source, target) in (
("van", "la"),
("la", "chi"),
("hou", "chi"),
("to", "mtl"),
("mtl", "bos"),
("nyc", "bos"),
("to", "hou"),
("to", "nyc"),
("la", "nyc"),
("nyc", "bos")
)
]
elements = vcat(nodes, edges)
app.layout = cyto_cytoscape(
id="cytoscape-layout-3",
elements=elements,
style=Dict("width" => "100%", "height" => "350px"),
layout=Dict(
"name" => "grid"
)
)
run_server(app, "0.0.0.0", debug=true)
Fine-tuning the Layouts
For any given name item, a collection of keys are accepted by the layout
dictionary. For example, the
grid layout
will accept row and cols, the
circle layout radius
and startAngle, and so forth. Here is the grid layout
with the same graph as above, but with different layout options:
using Dash, DashCytoscape
app = dash()
nodes = [
Dict(
"data" => Dict("id" => short, "label" => label),
"position" => Dict("x" => 20*lat, "y" => -20*long)
)
for (short, label, long, lat) in (
("la", "Los Angeles", 34.03, -118.25),
("nyc", "New York", 40.71, -74),
("to", "Toronto", 43.65, -79.38),
("mtl", "Montreal", 45.50, -73.57),
("van", "Vancouver", 49.28, -123.12),
("chi", "Chicago", 41.88, -87.63),
("bos", "Boston", 42.36, -71.06),
("hou", "Houston", 29.76, -95.37)
)
]
edges = [
Dict("data" => Dict("source" => source, "target" => target))
for (source, target) in (
("van", "la"),
("la", "chi"),
("hou", "chi"),
("to", "mtl"),
("mtl", "bos"),
("nyc", "bos"),
("to", "hou"),
("to", "nyc"),
("la", "nyc"),
("nyc", "bos")
)
]
elements = vcat(nodes, edges)
app.layout = cyto_cytoscape(
id="cytoscape-layout-4",
elements=elements,
style=Dict("width" => "100%", "height" => "350px"),
layout=Dict(
"name" => "grid",
"rows" => 3
)
)
run_server(app, "0.0.0.0", debug=true)
In the case of the circle layout, we can force the nodes to start and end
at a certain angle in radians:
using Dash, DashCytoscape
app = dash()
nodes = [
Dict(
"data" => Dict("id" => short, "label" => label),
"position" => Dict("x" => 20*lat, "y" => -20*long)
)
for (short, label, long, lat) in (
("la", "Los Angeles", 34.03, -118.25),
("nyc", "New York", 40.71, -74),
("to", "Toronto", 43.65, -79.38),
("mtl", "Montreal", 45.50, -73.57),
("van", "Vancouver", 49.28, -123.12),
("chi", "Chicago", 41.88, -87.63),
("bos", "Boston", 42.36, -71.06),
("hou", "Houston", 29.76, -95.37)
)
]
edges = [
Dict("data" => Dict("source" => source, "target" => target))
for (source, target) in (
("van", "la"),
("la", "chi"),
("hou", "chi"),
("to", "mtl"),
("mtl", "bos"),
("nyc", "bos"),
("to", "hou"),
("to", "nyc"),
("la", "nyc"),
("nyc", "bos")
)
]
elements = vcat(nodes, edges)
app.layout = cyto_cytoscape(
id="cytoscape-layout-5",
elements=elements,
style=Dict("width" => "100%", "height" => "350px"),
layout=Dict(
"name" => "circle",
"radius" => 250,
"startAngle" => pi * 1/6,
"sweep" => pi * 2/3
)
)
run_server(app, "0.0.0.0", debug=true)
For the breadthfirst layout, a tree is created from the existing nodes
by performing a breadth-first search of the graph. By default, the root(s)
of the tree is inferred, but can also be specified as an option. Here is
how the graph would look like if we choose New York City as the root:
using Dash, DashCytoscape
app = dash()
nodes = [
Dict(
"data" => Dict("id" => short, "label" => label),
"position" => Dict("x" => 20*lat, "y" => -20*long)
)
for (short, label, long, lat) in (
("la", "Los Angeles", 34.03, -118.25),
("nyc", "New York", 40.71, -74),
("to", "Toronto", 43.65, -79.38),
("mtl", "Montreal", 45.50, -73.57),
("van", "Vancouver", 49.28, -123.12),
("chi", "Chicago", 41.88, -87.63),
("bos", "Boston", 42.36, -71.06),
("hou", "Houston", 29.76, -95.37)
)
]
edges = [
Dict("data" => Dict("source" => source, "target" => target))
for (source, target) in (
("van", "la"),
("la", "chi"),
("hou", "chi"),
("to", "mtl"),
("mtl", "bos"),
("nyc", "bos"),
("to", "hou"),
("to", "nyc"),
("la", "nyc"),
("nyc", "bos")
)
]
elements = vcat(nodes, edges)
app.layout = cyto_cytoscape(
id="cytoscape-layout-6",
elements=elements,
style=Dict("width" => "100%", "height" => "350px"),
layout=Dict(
"name" => "breadthfirst",
"roots" => "[id = 'nyc']"
)
)
run_server(app, "0.0.0.0", debug=true)
Here is what would happen if we chose Montreal and Vancouver instead:
using Dash, DashCytoscape
app = dash()
nodes = [
Dict(
"data" => Dict("id" => short, "label" => label),
"position" => Dict("x" => 20*lat, "y" => -20*long)
)
for (short, label, long, lat) in (
("la", "Los Angeles", 34.03, -118.25),
("nyc", "New York", 40.71, -74),
("to", "Toronto", 43.65, -79.38),
("mtl", "Montreal", 45.50, -73.57),
("van", "Vancouver", 49.28, -123.12),
("chi", "Chicago", 41.88, -87.63),
("bos", "Boston", 42.36, -71.06),
("hou", "Houston", 29.76, -95.37)
)
]
edges = [
Dict("data" => Dict("source" => source, "target" => target))
for (source, target) in (
("van", "la"),
("la", "chi"),
("hou", "chi"),
("to", "mtl"),
("mtl", "bos"),
("nyc", "bos"),
("to", "hou"),
("to", "nyc"),
("la", "nyc"),
("nyc", "bos")
)
]
elements = vcat(nodes, edges)
app.layout = cyto_cytoscape(
id="cytoscape-layout-7",
elements=elements,
style=Dict("width" => "100%", "height" => "350px"),
layout=Dict(
"name" => "breadthfirst",
"roots" => "#van, #mtl"
)
)
run_server(app, "0.0.0.0", debug=true)
Notice here that we are not giving the ID of the nodes to the
roots
key, but instead using a specific syntax to select the desired elements.
This concept of selector is extensively documented in Cytoscape.js,
and will be further explored in part 3.
We follow the same syntax as the Javascript library.
For preset layouts, you can also specify the positions for which you would like to render each
of your nodes:
using Dash, DashCytoscape
app = dash()
nodes = [
Dict(
"data" => Dict("id" => short, "label" => label),
"position" => Dict("x" => 20*lat, "y" => -20*long)
)
for (short, label, long, lat) in (
("la", "Los Angeles", 34.03, -118.25),
("nyc", "New York", 40.71, -74),
("to", "Toronto", 43.65, -79.38),
("mtl", "Montreal", 45.50, -73.57),
("van", "Vancouver", 49.28, -123.12),
("chi", "Chicago", 41.88, -87.63),
("bos", "Boston", 42.36, -71.06),
("hou", "Houston", 29.76, -95.37)
)
]
edges = [
Dict("data" => Dict("source" => source, "target" => target))
for (source, target) in (
("van", "la"),
("la", "chi"),
("hou", "chi"),
("to", "mtl"),
("mtl", "bos"),
("nyc", "bos"),
("to", "hou"),
("to", "nyc"),
("la", "nyc"),
("nyc", "bos")
)
]
elements = vcat(nodes, edges)
app.layout = cyto_cytoscape(
id="cytoscape-layout-8",
elements=elements,
style=Dict("width" => "100%", "height" => "350px"),
layout=Dict(
"name" => "preset",
"positions" => Dict(
node["data"]["id"] => node["position"]
for node in nodes
)
)
)
run_server(app, "0.0.0.0", debug=true)
In the callbacks chapter, you will learn how to interactively update your layout; in order
to usepreset, you will need to specify the position of each node.
Physics-based Layouts
Additionally, the cose layout can be used to position the nodes using
a force-directed layout by simulating attraction and repulsion among the
elements, based on the paper by
Dogrusoz et al, 2009.
using Dash, DashCytoscape
app = dash()
nodes = [
Dict(
"data" => Dict("id" => short, "label" => label),
"position" => Dict("x" => 20*lat, "y" => -20*long)
)
for (short, label, long, lat) in (
("la", "Los Angeles", 34.03, -118.25),
("nyc", "New York", 40.71, -74),
("to", "Toronto", 43.65, -79.38),
("mtl", "Montreal", 45.50, -73.57),
("van", "Vancouver", 49.28, -123.12),
("chi", "Chicago", 41.88, -87.63),
("bos", "Boston", 42.36, -71.06),
("hou", "Houston", 29.76, -95.37)
)
]
edges = [
Dict("data" => Dict("source" => source, "target" => target))
for (source, target) in (
("van", "la"),
("la", "chi"),
("hou", "chi"),
("to", "mtl"),
("mtl", "bos"),
("nyc", "bos"),
("to", "hou"),
("to", "nyc"),
("la", "nyc"),
("nyc", "bos")
)
]
elements = vcat(nodes, edges)
app.layout = cyto_cytoscape(
id="cytoscape-layout-9",
elements=elements,
style=Dict("width" => "100%", "height" => "350px"),
layout=Dict(
"name" => "cose"
)
)
run_server(app, "0.0.0.0", debug=true)