From 43c4ea65d7116c762e7cea13745687acf2c5a41a Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Herv=C3=A9=20=20MENAGER?= <herve.menager@pasteur.fr>
Date: Sun, 6 May 2018 21:56:24 +0200
Subject: [PATCH] save and display the PCA correlation circle
Former-commit-id: 42b2da5f48c598d4075607c9a59ae18ff65df1be
---
ippisite/ippidb/management/commands/pca.py | 13 ++++++++++---
ippisite/ippidb/templates/compound_card.html | 8 ++++++++
ippisite/ippidb/views.py | 10 +++++++---
3 files changed, 25 insertions(+), 6 deletions(-)
diff --git a/ippisite/ippidb/management/commands/pca.py b/ippisite/ippidb/management/commands/pca.py
index d50e9cc3..ea84a9e6 100644
--- a/ippisite/ippidb/management/commands/pca.py
+++ b/ippisite/ippidb/management/commands/pca.py
@@ -1,5 +1,7 @@
import glob
import json
+import io
+import base64
from django.core.management import BaseCommand, CommandError
from django.forms.models import model_to_dict
@@ -51,6 +53,7 @@ class Command(BaseCommand):
x = StandardScaler().fit_transform(x)
pca = PCA(n_components=2)
principal_components = pca.fit_transform(x)
+ # compute correlation circle
variance_ratio = pd.Series(pca.explained_variance_ratio_)
coef = np.transpose(pca.components_)
cols = ['PC-'+str(x) for x in range(len(variance_ratio))]
@@ -69,13 +72,17 @@ class Command(BaseCommand):
plt.ylabel("PC-1 (%s%%)" % str(variance_ratio[1])[:4].lstrip("0."))
plt.xlim((-1,1))
plt.ylim((-1,1))
- plt.title("Circle of Correlations")
- plt.savefig('foo2.png')
+ my_string_io_bytes = io.BytesIO()
+ plt.savefig(my_string_io_bytes, format='png')
+ my_string_io_bytes.seek(0)
+ # figdata_png is the correlation circle figure, base 64-encoded
+ figdata_png = base64.b64encode(my_string_io_bytes.read())
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=(',',':'))
+ pca_data_cc = {'data': pca_data, 'correlation_circle': figdata_png.decode("utf-8")}
+ pca_json = json.dumps(pca_data_cc, separators=(',',':'))
new = PcaBiplotData()
new.pca_biplot_data = pca_json
new.save()
diff --git a/ippisite/ippidb/templates/compound_card.html b/ippisite/ippidb/templates/compound_card.html
index 3a8b425d..d3007bb7 100644
--- a/ippisite/ippidb/templates/compound_card.html
+++ b/ippisite/ippidb/templates/compound_card.html
@@ -158,6 +158,7 @@
</div>
</div>
</div>
+ <div class="row">
<div class="card col-sm-12 col-md-6">
<h5 class="card-header">PCA : iPPI-DB chemical space</h5>
<div class="card-body">
@@ -166,9 +167,16 @@
<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 class="card col-sm-12 col-md-6">
+ <h5 class="card-header">PCA : Correlation circle</h5>
+ <div class="card-body">
+ <img src="data:image/png;base64,{{ pca_biplot_cc }}"\>
+ </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">
<h5 class="card-header">Efficiencies: iPPI-DB biplot LE versus LLE</h5>
diff --git a/ippisite/ippidb/views.py b/ippisite/ippidb/views.py
index 42c4b1f1..0988d80c 100644
--- a/ippisite/ippidb/views.py
+++ b/ippisite/ippidb/views.py
@@ -1,9 +1,11 @@
-import ippidb
+import json
from django.shortcuts import render
from django.http import HttpResponseRedirect, Http404
from django.core.paginator import Paginator, EmptyPage, PageNotAnInteger
from formtools.wizard.views import SessionWizardView, NamedUrlSessionWizardView
+
+import ippidb
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, PcaBiplotData
from .ws import get_pdb_uniprot_mapping
@@ -238,5 +240,7 @@ def compound_card(request, compound_id):
except Compound.DoesNotExist:
raise Http404("No compound data for %s:%s" % (compound_id))
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})
+ pca_biplot = json.loads(PcaBiplotData.objects.get().pca_biplot_data)
+ pca_biplot_data = json.dumps(pca_biplot['data'])
+ pca_biplot_cc = pca_biplot['correlation_circle']
+ return render(request, 'compound_card.html', {'compound': compound, 'le_lle_biplot_data': le_lle_biplot_data, 'pca_biplot_data': pca_biplot_data, 'pca_biplot_cc': pca_biplot_cc})
--
GitLab