diff --git a/ippisite/db.sqlite3.REMOVED.git-id b/ippisite/db.sqlite3.REMOVED.git-id
index 0fc6bb90b007a4760562c0146ef75c5b7f91ee15..0a4ddca2744d40f0c00924b4682b70f92643fba6 100644
--- a/ippisite/db.sqlite3.REMOVED.git-id
+++ b/ippisite/db.sqlite3.REMOVED.git-id
@@ -1 +1 @@
-5fb9ed7a41b37ceaa343fd897c2db6c4123dfea8
\ No newline at end of file
+9bc693989d626dd0e41c7e205c09395148196f5f
\ No newline at end of file
diff --git a/ippisite/ippidb/management/commands/pca.py b/ippisite/ippidb/management/commands/pca.py
new file mode 100644
index 0000000000000000000000000000000000000000..ffd86af4cf8caf1fcbcaaa45a3432ce4238f347f
--- /dev/null
+++ b/ippisite/ippidb/management/commands/pca.py
@@ -0,0 +1,55 @@
+import glob
+import json
+
+from django.core.management import BaseCommand, CommandError
+from django.forms.models import model_to_dict
+import pandas as pd
+from sklearn.decomposition import PCA
+from sklearn.preprocessing import StandardScaler
+
+from ippidb.models import Compound, PcaBiplotData
+
+class Command(BaseCommand):
+
+ help = "Generate the data for the compound LE vs LLE biplot"
+
+ def handle(self, *args, **options):
+ self.stdout.write(self.style.SUCCESS('Generating the PCA biplot...'))
+ pca_data = []
+ features = ['aromatic_ratio', 'balaban_index', 'fsp3',
+ 'gc_molar_refractivity', 'log_d', 'a_log_p',
+ 'mean_atom_vol_vdw', 'molecular_weight', 'nb_acceptor_h',
+ 'nb_aliphatic_amines', 'nb_aromatic_bonds',
+ 'nb_aromatic_ether', 'nb_aromatic_sssr', 'nb_atom',
+ 'nb_atom_non_h', 'nb_benzene_like_rings', 'nb_bonds',
+ 'nb_bonds_non_h', 'nb_br', 'nb_c', 'nb_chiral_centers',
+ 'nb_circuits', 'nb_cl', 'nb_csp2', 'nb_csp3', 'nb_donor_h',
+ 'nb_double_bonds', 'nb_f', 'nb_i', 'nb_multiple_bonds',
+ 'nb_n', 'nb_o', 'nb_rings', 'nb_rotatable_bonds',
+ 'randic_index', 'rdf070m', 'rotatable_bond_fraction',
+ 'sum_atom_polar', 'sum_atom_vol_vdw', 'tpsa', 'ui',
+ 'wiener_index']
+ PcaBiplotData.objects.all().delete()
+ self.stdout.write(
+ self.style.SUCCESS('Successfully flushed PCA biplot data'))
+ l = []
+ for comp in Compound.objects.all():
+ values = model_to_dict(comp, fields=features + ['id','family'])
+ values['family'] = comp.best_pXC50_activity_ppi_family
+ l.append(values)
+ df = pd.DataFrame(l)
+ x = df.loc[:, features].values
+ y = df.loc[:,['family']].values
+ x = StandardScaler().fit_transform(x)
+ pca = PCA(n_components=2)
+ principal_components = pca.fit_transform(x)
+ principal_df = pd.DataFrame(data = principal_components , columns = ['x', 'y'])
+ final_df = pd.concat([principal_df, df[['family','id']]], axis = 1)
+ for index, row in final_df.iterrows():
+ pca_data.append({'x': row.x, 'y': row.y, 'id': row.id, 'family_name': row.family})
+ pca_json = json.dumps(pca_data, separators=(',',':'))
+ new = PcaBiplotData()
+ new.pca_biplot_data = pca_json
+ new.save()
+ self.stdout.write(
+ self.style.SUCCESS('Successfully generated PCA biplot data'))
diff --git a/ippisite/ippidb/migrations/0034_auto_20180503_2110.py b/ippisite/ippidb/migrations/0034_auto_20180503_2110.py
new file mode 100644
index 0000000000000000000000000000000000000000..5ed85ffcfb119b739ca489ab8e9a80e6fec9391e
--- /dev/null
+++ b/ippisite/ippidb/migrations/0034_auto_20180503_2110.py
@@ -0,0 +1,26 @@
+# -*- coding: utf-8 -*-
+# Generated by Django 1.11 on 2018-05-03 21:10
+from __future__ import unicode_literals
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+ dependencies = [
+ ('ippidb', '0033_auto_20180502_1500'),
+ ]
+
+ operations = [
+ migrations.CreateModel(
+ name='PcaBiplotData',
+ fields=[
+ ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+ ('pca_biplot_data', models.CharField(blank=True, max_length=150000, null=True, verbose_name='PCA biplot JSON data')),
+ ],
+ ),
+ migrations.AlterModelOptions(
+ name='ppifamily',
+ options={'verbose_name_plural': 'PPI Families'},
+ ),
+ ]
diff --git a/ippisite/ippidb/models.py b/ippisite/ippidb/models.py
index 2a14d8ca42b9e6a9637d8e36da63e99dc0583777..7d2276d2fb4a42b9e14185a480f90eee761a13ae 100644
--- a/ippisite/ippidb/models.py
+++ b/ippisite/ippidb/models.py
@@ -493,6 +493,9 @@ class Compound(models.Model):
return list(set([ca.ppi.family for ca in self.compoundaction_set.all()]))
+class PcaBiplotData(models.Model):
+ pca_biplot_data = models.CharField('PCA biplot JSON data', max_length=150000, blank=True, null=True)
+
class LeLleBiplotData(models.Model):
le_lle_biplot_data = models.CharField('LE-LLE biplot JSON data', max_length=150000, blank=True, null=True)
diff --git a/ippisite/ippidb/templates/base.html b/ippisite/ippidb/templates/base.html
index 2658a79ca5ca20ef5c0d3f5d6238865c8dd59212..5e37787e9c2543048b0d9b02b4668ed4de87e2b6 100644
--- a/ippisite/ippidb/templates/base.html
+++ b/ippisite/ippidb/templates/base.html
@@ -93,7 +93,7 @@
data: radarChartData,
options: { scaleLineWidth : 1, pointLabelFontFamily : "'Helvetica Neue'", pointLabelFontSize : 12, scaleOverride : true, scaleSteps : 5, scaleStepWidth : 0.2}});
};
- var drawLeLleBiplotChart = function(canvasId, compoundId, compoundFamily, plotData, tabHash){
+ var drawCompoundsBiplotChart = function(canvasId, compoundId, compoundFamily, plotData, tabHash){
var currentCompoundData = [];
var currentFamilyData = [];
var otherFamiliesData = [];
diff --git a/ippisite/ippidb/templates/compound_card.html b/ippisite/ippidb/templates/compound_card.html
index e3ecb6d58c59312eb46e18a96435a3c3083bf953..4f19cd73f248837440aab126cabc043c6a563144 100644
--- a/ippisite/ippidb/templates/compound_card.html
+++ b/ippisite/ippidb/templates/compound_card.html
@@ -158,6 +158,17 @@
</div>
</div>
</div>
+ <div class="card col-sm-12 col-md-6">
+ <h5 class="card-header">PCA : iPPI-DB chemical space</h5>
+ <div class="card-body">
+
+ <canvas id="pca_biplot"></canvas>
+ <script>
+ drawCompoundsBiplotChart('pca_biplot', {{ compound.id }}, '{{ compound.best_pXC50_activity_ppi_family|default_if_none:"No target family identified" }}', {{ pca_biplot_data | safe }}, 'physicochemistry');
+ </script>
+ </div>
+ </div>
+ </div>
</div>
<div class="tab-pane fade" id="pharmacology" role="tabpanel" aria-labelledby="pharmacology-tab">
<div class="card col-sm-12 col-md-12">
@@ -165,7 +176,7 @@
<div class="card-body">
<canvas id="le_lle_biplot"></canvas>
<script>
- drawLeLleBiplotChart('le_lle_biplot', {{ compound.id }}, '{{ compound.best_pXC50_activity_ppi_family|default_if_none:"No target family identified" }}', {{ biplot_data | safe }}, 'pharmacology');
+ drawCompoundsBiplotChart('le_lle_biplot', {{ compound.id }}, '{{ compound.best_pXC50_activity_ppi_family|default_if_none:"No target family identified" }}', {{ le_lle_biplot_data | safe }}, 'pharmacology');
</script>
</div>
</div>
diff --git a/ippisite/ippidb/views.py b/ippisite/ippidb/views.py
index a8cabb85a616bbbabb21b9d3cd507ba6200a1cfe..42c4b1f15f87c8583ae5e1fa2423b14f478ff361 100644
--- a/ippisite/ippidb/views.py
+++ b/ippisite/ippidb/views.py
@@ -5,7 +5,7 @@ from django.http import HttpResponseRedirect, Http404
from django.core.paginator import Paginator, EmptyPage, PageNotAnInteger
from formtools.wizard.views import SessionWizardView, NamedUrlSessionWizardView
from .forms import IdForm, BibliographyForm, PDBForm, ProteinForm, ComplexCompositionForm, ComplexCompositionFormSet, ProteinDomainComplexTypeForm, ProteinDomainComplexForm, PpiForm, PpiComplexForm, PpiAndComplexForm, ProteinFormSet,TestsForm, CompoundForm, CompoundFormSet
-from .models import Protein, Bibliography, ProteinDomainComplex, ProteinDomainBoundComplex, RefCompoundBiblio, TestActivityDescription, Compound, Ppi, Disease, Taxonomy, LeLleBiplotData
+from .models import Protein, Bibliography, ProteinDomainComplex, ProteinDomainBoundComplex, RefCompoundBiblio, TestActivityDescription, Compound, Ppi, Disease, Taxonomy, LeLleBiplotData, PcaBiplotData
from .ws import get_pdb_uniprot_mapping
@@ -237,5 +237,6 @@ def compound_card(request, compound_id):
compound = Compound.objects.get(id=int(compound_id))
except Compound.DoesNotExist:
raise Http404("No compound data for %s:%s" % (compound_id))
- biplot_data = LeLleBiplotData.objects.get().le_lle_biplot_data
- return render(request, 'compound_card.html', {'compound': compound, 'biplot_data': biplot_data})
+ le_lle_biplot_data = LeLleBiplotData.objects.get().le_lle_biplot_data
+ pca_biplot_data = PcaBiplotData.objects.get().pca_biplot_data
+ return render(request, 'compound_card.html', {'compound': compound, 'le_lle_biplot_data': le_lle_biplot_data, 'pca_biplot_data': pca_biplot_data})
diff --git a/ippisite/requirements.txt b/ippisite/requirements.txt
index 946f211d485f5286315e614d64727c9bfa2d1e4d..1c592c35804d1067cb189830b450f3caaf08cd95 100644
--- a/ippisite/requirements.txt
+++ b/ippisite/requirements.txt
@@ -12,3 +12,5 @@ django-debug-toolbar
mod_wsgi
bioblend
django-allauth
+sklearn
+scipy