Add utility for loading as a graph

References #35

docs/graph.md

@@ -0,0 +1,9 @@
+---
+layout: page
+title: Graph
+permalink: /graph/
+---
+This chart shows various aspects of the positive mappings graph. Larger components means that more extensive curation
+has been done. Higher density components means that they have been checked multiple times.
+
+<img src="https://raw.githubusercontent.com/biomappings/biomappings/main/docs/img/components.png" alt="Comparison"/>

setup.cfg

@@ -38,6 +38,7 @@ keywords =
 
 [options]
 install_requires =
+    networkx
     requests
     click
     pyyaml

src/biomappings/graph.py

@@ -0,0 +1,72 @@
+# -*- coding: utf-8 -*-
+
+"""Load Biomappings as a graph."""
+
+import os
+
+import matplotlib.pyplot as plt
+import networkx as nx
+import seaborn as sns
+
+from biomappings.resources import load_mappings
+from biomappings.utils import IMG, MiriamValidator
+
+
+def get_positive_graph() -> nx.Graph:
+    """Get a graph of the positive mappings."""
+    v = MiriamValidator()
+    graph = nx.Graph()
+    for mapping in load_mappings():
+        source_curie = v.get_curie(mapping['source prefix'], mapping['source identifier'])
+        graph.add_node(
+            source_curie,
+            prefix=mapping['source prefix'],
+            identifier=mapping['source identifier'],
+            name=mapping['source name'],
+        )
+        target_curie = v.get_curie(mapping['target prefix'], mapping['target identifier'])
+        graph.add_node(
+            target_curie,
+            prefix=mapping['target prefix'],
+            identifier=mapping['target identifier'],
+            name=mapping['target name'],
+        )
+        graph.add_edge(
+            source_curie,
+            target_curie,
+            provenance=mapping['source'],
+            type=mapping['type'],
+        )
+    return graph
+
+
+def _main():
+    fig, axes = plt.subplots(1, 3, figsize=(10, 3.5))
+    graph = get_positive_graph()
+
+    sizes = [len(c) for c in nx.connected_components(graph)]
+    sns.histplot(sizes, ax=axes[0])
+    axes[0].set_yscale('log')
+    axes[0].set_title('Component Node Sizes')
+
+    sizes = [graph.subgraph(c).number_of_edges() for c in nx.connected_components(graph)]
+    sns.histplot(sizes, ax=axes[1])
+    axes[1].set_yscale('log')
+    axes[1].set_title('Component Edge Sizes')
+    axes[1].set_ylabel('')
+
+    densities = [nx.density(graph.subgraph(c)) for c in nx.connected_components(graph)]
+    sns.histplot(densities, ax=axes[2], kde=True)
+    axes[2].set_xlim([0.0, 1.0])
+    axes[2].set_title('Component Densities')
+    axes[2].set_ylabel('')
+
+    path = os.path.join(IMG, 'components.png')
+    print('saving to', path)
+    plt.tight_layout()
+    plt.savefig(path, dpi=300)
+    plt.close(fig)
+
+
+if __name__ == '__main__':
+    _main()

src/biomappings/resources/__init__.py

@@ -7,9 +7,8 @@
 import os
 from typing import Dict, Iterable, List, Mapping, Sequence, Tuple
 
-from biomappings.utils import get_canonical_tuple
+from biomappings.utils import RESOURCE_PATH, get_canonical_tuple
 
-RESOURCE_PATH = os.path.dirname(os.path.abspath(__file__))
 MAPPINGS_HEADER = [
     'source prefix',
     'source identifier',

src/biomappings/utils.py

@@ -9,6 +9,10 @@
 
 import requests
 
+HERE = os.path.dirname(os.path.abspath(__file__))
+RESOURCE_PATH = os.path.abspath(os.path.join(HERE, 'resources'))
+IMG = os.path.abspath(os.path.join(HERE, os.pardir, os.pardir, 'docs', 'img'))
+
 
 def get_git_hash() -> Optional[str]:
     """Get the git hash.