#!/usr/bin/env python
# coding: utf-8

# In[2]:


from ontobio.ontol_factory import OntologyFactory

# Create ontology object, for mammalian phenotype ontology
# Transparently uses remote SPARQL service.
# (May take a few seconds to run first time, Jupyter will show '*'. BE PATIENT, do
# not re-execute cell)
ofactory = OntologyFactory()
ont = ofactory.create('mp')


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from ontobio.assoc_factory import AssociationSetFactory

MOUSE = 'NCBITaxon:10090'

# Create association set
# Transparently uses remote Monarch service.
# (May take a few seconds to run first time, Jupyter will show '*'. BE PATIENT, do
# not re-execute cell)
afactory = AssociationSetFactory()
aset = afactory.create(ontology=ont,
                       subject_category='gene',
                       object_category='phenotype',
                       taxon=MOUSE)


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[p1] = ont.search("abnormal hippocampus morphology")
[p2] = ont.search("abnormal glucose homeostasis")


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genes = aset.query([p1, p2])


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len(genes)


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genes


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["{} '{}'".format(g, aset.label(g)) for g in genes]


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z, xlabels, ylabels = aset.similarity_matrix(genes, genes)


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import plotly.plotly as py
import plotly.graph_objs as go
import numpy as np


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trace = go.Heatmap(z=-np.array(z),
                       x=xlabels,
                       y=ylabels)


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py.iplot([trace], filename='labelled-heatmap')


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