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English labels for influence map #76

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English labels for influence map #76

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4a36208
In influence map, use English labels instead of PySB rule labels
djmilstein May 12, 2018
6437d6c
Add the PySB label underneath the English label because a single stat…
djmilstein May 12, 2018
ac01650
Only include the PySB rule in the influence map labels if needed to d…
djmilstein May 12, 2018
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85 changes: 76 additions & 9 deletions bioagents/mra/mra.py
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Original file line number Diff line number Diff line change
Expand Up @@ -20,6 +20,7 @@
from pysb.tools import render_reactions
from pysb.export import export
from indra.util.kappa_util import im_json_to_graph, cm_json_to_graph
from indra.assemblers.english_assembler import EnglishAssembler


logger = logging.getLogger('MRA')
Expand Down Expand Up @@ -64,7 +65,8 @@ def build_model_from_ekb(self, model_ekb):
res['ambiguities'] = ambiguities
model_exec = self.assemble_pysb(stmts)
res['model_exec'] = model_exec
res['diagrams'] = make_diagrams(model_exec, model_id)
res['diagrams'] = make_diagrams(model_exec, model_id,
self.models[model_id])
return res

def build_model_from_json(self, model_json):
Expand All @@ -77,7 +79,8 @@ def build_model_from_json(self, model_json):
return res
model_exec = self.assemble_pysb(stmts)
res['model_exec'] = model_exec
res['diagrams'] = make_diagrams(model_exec, model_id)
res['diagrams'] = make_diagrams(model_exec, model_id,
self.models[model_id])
return res

def expand_model_from_ekb(self, model_ekb, model_id):
Expand All @@ -99,7 +102,8 @@ def expand_model_from_ekb(self, model_ekb, model_id):
res['model_new'] = new_stmts
model_exec = self.assemble_pysb(model_stmts)
res['model_exec'] = model_exec
res['diagrams'] = make_diagrams(model_exec, new_model_id)
res['diagrams'] = make_diagrams(model_exec, new_model_id,
self.models[model_id])
return res

def expand_model_from_json(self, model_json, model_id):
Expand All @@ -116,7 +120,8 @@ def expand_model_from_json(self, model_json, model_id):
res['model_new'] = new_stmts
model_exec = self.assemble_pysb(model_stmts)
res['model_exec'] = model_exec
res['diagrams'] = make_diagrams(model_exec, new_model_id)
res['diagrams'] = make_diagrams(model_exec, new_model_id,
self.models[model_id])
return res

def has_mechanism(self, mech_ekb, model_id):
Expand Down Expand Up @@ -159,7 +164,8 @@ def remove_mechanism(self, mech_ekb, model_id):
res['model_exec'] = model_exec
if removed_stmts:
res['removed'] = removed_stmts
res['diagrams'] = make_diagrams(model_exec, model_id)
res['diagrams'] = make_diagrams(model_exec, model_id,
self.models[model_id])
self.new_model(new_stmts)
return res

Expand All @@ -181,7 +187,8 @@ def model_undo(self):
if not stmts:
return res
res['ambiguities'] = []
res['diagrams'] = make_diagrams(model_exec, new_model_id)
res['diagrams'] = make_diagrams(model_exec, new_model_id,
self.models[new_model_id])
return res

def get_upstream(self, target, model_id):
Expand Down Expand Up @@ -249,11 +256,11 @@ def get_ambiguities(tp):
return all_ambiguities


def make_diagrams(pysb_model, model_id):
def make_diagrams(pysb_model, model_id, indra_model):
sbgn = make_sbgn(pysb_model, model_id)
rxn = draw_reaction_network(pysb_model, model_id)
cm = draw_contact_map(pysb_model, model_id)
im = draw_influence_map(pysb_model, model_id)
im = draw_influence_map(pysb_model, model_id, indra_model)
diagrams = {'reactionnetwork': rxn, 'contactmap': cm,
'influencemap': im, 'sbgn': sbgn}
return diagrams
Expand All @@ -272,10 +279,12 @@ def make_sbgn(pysb_model, model_id):
return sbgn_str


def draw_influence_map(pysb_model, model_id):
def draw_influence_map(pysb_model, model_id, indra_model):
"""Generate a Kappa influence map, draw it and save it as a PNG."""
try:
im = make_influence_map(pysb_model)
im = make_influence_map_labels_natural_language(im, pysb_model,
indra_model)
fname = 'model%d_im' % model_id
abs_path = os.path.abspath(os.getcwd())
full_path = os.path.join(abs_path, fname + '.png')
Expand Down Expand Up @@ -304,6 +313,64 @@ def make_influence_map(pysb_model):
return im


def get_statement_by_uuid(statements, uuid):
"""Returns the first statement in statements with the given uuid, or None
if no such statements are in the provided list."""
for statement in statements:
if statement.uuid == uuid:
return statement
return None


def dict_value_appears_multiple_times(d, value):
"""Returns True iff the given value is mapped to multiple times in this
dictionary."""
count = 0
for k, v in d.items():
if v == value:
count += 1
return count > 1

def make_influence_map_labels_natural_language(im, pysb_model, indra_model):
"""Replaces the labels of the influence map with natural language labels.
"""
# Get the name of all the rules in the pysb model
rule_names = [rule.name for rule in pysb_model.rules]

relabel_map_english = {}
relabel_map_english_and_rule = {}
for annotation in pysb_model.annotations:
if annotation.subject in rule_names:
name = annotation.subject
if annotation.predicate == 'from_indra_statement':
# We found the INDRA statement uuid corresponding to a rule
statement_uuid = annotation.object
s = get_statement_by_uuid(indra_model, statement_uuid)

# Convert the statement into English
assembler = EnglishAssembler([s])

english_text = assembler.make_model()
english_and_rule = english_text + ' (' + name + ')'

relabel_map_english[name] = english_text
relabel_map_english_and_rule[name] = english_and_rule

# Use only the English text if that is unambiguous, otherwise include
# the rule name too
relabel_map = {}
for before in relabel_map_english:
english_text = relabel_map_english[before]
if dict_value_appears_multiple_times(relabel_map_english,
english_text):
relabel_map[before] = relabel_map_english_and_rule[before]
else:
relabel_map[before] = english_text

im = networkx.relabel_nodes(im, relabel_map)
return im


def draw_contact_map(pysb_model, model_id):
try:
cm = make_contact_map(pysb_model)
Expand Down
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