Source code for

#!/usr/bin/env python

Usage: ``python -m >``

If your model uses species as expression rates, you can visualize
these interactions by including the --include-rate-species option::

    python -m --include-rate-species >

Renders the reactions produced by a model into the "dot" graph format which can
be visualized with Graphviz.

To create a PDF from the .dot file, use the "dot" command from Graphviz::

    dot -T pdf -O

This will create You can also change the "dot" command to one
of the other Graphviz drawing tools for a different type of layout. Note that
you can pipe the output of render_reactions straight into Graphviz without
creating an intermediate .dot file, which is especially helpful if you are
making continuous changes to the model and need to visualize your changes

    python -m | dot -T pdf -o mymodel.pdf

Note that some PDF viewers will auto-reload a changed PDF, so you may not even
need to manually reopen it every time you rerun the tool.

Output for Robertson example model

The Robertson example model (in ``pysb.examples.robertson``) contains
the following three reactions:

* A -> B
* B + B -> B + C
* C + B -> C + A

The reaction network diagram for this system as generated by this module and
rendered using ``dot`` is shown below:

.. image:: robertson_reactions.png
   :align: center
   :alt: Reaction network for pysb.examples.robertson

Circular nodes (``r0``, ``r1`` and ``r2``) indicate reactions; square nodes
(``A()``, ``B()`` and ``C()``) indicate species. Incoming arrows from a species
node to a reaction node indicate that the species is a reactant; outgoing
arrows from a reaction node to a species node indicate that the species is a
product. A hollow diamond-tipped arrow from a species to a reaction indicates
that the species is involved as both a reactant and a product, i.e., it serves
as a "modifier" (enzyme or catalyst).


import pysb
import pysb.bng
import re
import sys
import os
    import pygraphviz
except ImportError:
    pygraphviz = None

[docs]def run(model, include_rate_species=False): """ Render the reactions produced by a model into the "dot" graph format. Parameters ---------- model : pysb.core.Model The model to render. include_rate_species : bool If True, enable multigraph and add dashed edges from species used in expression rates to the node representing the reaction. Returns ------- string The dot format output. """ if pygraphviz is None: raise ImportError('pygraphviz library is required to run this ' 'function') pysb.bng.generate_equations(model) # Enable multigraph when include_rate_species is True strict = True if include_rate_species: strict = False graph = pygraphviz.AGraph(directed=True, rankdir="LR", strict=strict) ic_species = [ic.pattern for ic in model.initials] for i, cp in enumerate(model.species): species_node = 's%d' % i slabel = re.sub(r'% ', r'%\\l', str(cp)) slabel += '\\l' color = "#ccffcc" # color species with an initial condition differently if len([s for s in ic_species if s.is_equivalent_to(cp)]): color = "#aaffff" graph.add_node(species_node, label=slabel, shape="Mrecord", fillcolor=color, style="filled", color="transparent", fontsize="12", margin="0.06,0") for i, reaction in enumerate(model.reactions_bidirectional): reaction_node = 'r%d' % i graph.add_node(reaction_node, label=reaction_node, shape="circle", fillcolor="lightgray", style="filled", color="transparent", fontsize="12", width=".3", height=".3", margin="0.06,0") reactants = set(reaction['reactants']) products = set(reaction['products']) modifiers = reactants & products reactants = reactants - modifiers products = products - modifiers attr_reversible = {'dir': 'both', 'arrowtail': 'empty'} if reaction['reversible'] else {} rule = model.rules.get(reaction['rule'][0]) # Add a dashed edge when reaction forward and/or reverse parameters are # expressions that contain observables if include_rate_species: sps_forward = set() if isinstance(rule.rate_forward, pysb.core.Expression): sps_forward = sp_from_expression(rule.rate_forward) for s in sps_forward: r_link(graph, s, i, **{'style': 'dashed'}) if isinstance(rule.rate_reverse, pysb.core.Expression): sps_reverse = sp_from_expression(rule.rate_reverse) # Don't add edges that were added with forward parameters sps_reverse = sps_reverse - sps_forward for s in sps_reverse: r_link(graph, s, i, **{'style': 'dashed'}) for s in reactants: r_link(graph, s, i, **attr_reversible) for s in products: r_link(graph, s, i, _flip=True, **attr_reversible) for s in modifiers: r_link(graph, s, i, arrowhead="odiamond") return graph.string()
def r_link(graph, s, r, **attrs): nodes = ('s%d' % s, 'r%d' % r) if attrs.get('_flip'): del attrs['_flip'] nodes = reversed(nodes) attrs.setdefault('arrowhead', 'normal') graph.add_edge(*nodes, **attrs) def sp_from_expression(expression): expr_sps = [] for a in expression.expr.atoms(): if isinstance(a, pysb.core.Observable): sps = a.species expr_sps += sps return set(expr_sps) usage = __doc__ usage = usage[1:] # strip leading newline if __name__ == '__main__': # sanity checks on filename if len(sys.argv) <= 1: print(usage, end=' ') exit() model_filename = sys.argv[-1] if not os.path.exists(model_filename): raise Exception("File '%s' doesn't exist" % model_filename) if not'\.py$', model_filename): raise Exception("File '%s' is not a .py file" % model_filename) sys.path.insert(0, os.path.dirname(model_filename)) model_name = re.sub(r'\.py$', '', os.path.basename(model_filename)) # import it try: # FIXME if the model has the same name as some other "real" module # which we use, there will be trouble # (use the imp package and import as some safe name?) model_module = __import__(model_name) except Exception as e: print("Error in model script:\n") raise # grab the 'model' variable from the module try: model = model_module.__dict__['model'] except KeyError: raise Exception("File '%s' isn't a model file" % model_filename) include_rate_species = False if '--include-rate-species' in sys.argv: include_rate_species = True print(run(model, include_rate_species))