Layouts for displaying regulatory graphs

import biolqm
import ginsim

Layouts for displaying regulatory graphs#

Small model#

lqm = biolqm.load("http://ginsim.org/sites/default/files/phageLambda4.zginml")

Downloading http://ginsim.org/sites/default/files/phageLambda4.zginml

By default, the layout is performed with neato:

lrg = biolqm.to_ginsim(lqm)
ginsim.show(lrg)

The layout can be modified with biolqm.autolayout, using the method parameter. The methods are the one supported by GraphViz, which include dot, neato, circo, fdp, twopi, pathwork, osage, and sfdp (for large graphs). Scaling can be adjusted with the scale parameter.

biolqm.autolayout(lqm, method="patchwork")
lrg = biolqm.to_ginsim(lqm)
ginsim.show(lrg)

The layout can also be specifed at the (first) call to to_ginsim with the layout_method parameter:

lqm = biolqm.load("http://ginsim.org/sites/default/files/phageLambda4.zginml")
lrg = biolqm.to_ginsim(lqm, layout_method="circo")
ginsim.show(lrg)

Downloading http://ginsim.org/sites/default/files/phageLambda4.zginml

Medium size models#

lqm2 = biolqm.load("http://ginsim.org/sites/default/files/SuppMat_Model_Master_Model.zginml")
lrg = biolqm.to_ginsim(lqm2)
ginsim.show(lrg)

Downloading http://ginsim.org/sites/default/files/SuppMat_Model_Master_Model.zginml

biolqm.autolayout(lqm2, method="patchwork")
lrg = biolqm.to_ginsim(lqm2)
ginsim.show(lrg)

Large models#

lqm3 = biolqm.load("https://research.cellcollective.org/?dashboard=true#2171:1/t-cell-receptor-signaling/1")
lqm3 = biolqm.sanitize(lqm3)
lrg = biolqm.to_ginsim(lqm3, layout_scale=0.55)
ginsim.show(lrg)

Downloading http://api.cellcollective.org/model/export/2171?type=SBML

biolqm.autolayout(lqm3, method="patchwork")
lrg = biolqm.to_ginsim(lqm3)
ginsim.show(lrg)
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