diff options
| author | Jarrod Millman <jarrod.millman@gmail.com> | 2020-11-24 15:44:05 -0800 |
|---|---|---|
| committer | GitHub <noreply@github.com> | 2020-11-24 15:44:05 -0800 |
| commit | 1b390c8314ec188b1702c8419a650baa2c376601 (patch) | |
| tree | 36e68e2c7d5f0bdc55180bf4136a5d59f31a8a0a /examples | |
| parent | 001b37b55d03479303674a1a5d25256986a6f330 (diff) | |
| download | networkx-1b390c8314ec188b1702c8419a650baa2c376601.tar.gz | |
Add gene-gene network (#4269)
Diffstat (limited to 'examples')
| -rw-r--r-- | examples/algorithms/WormNet.v3.benchmark.txt | 78736 | ||||
| -rw-r--r-- | examples/algorithms/plot_betweenness_centrality.py | 83 |
2 files changed, 78819 insertions, 0 deletions
diff --git a/examples/algorithms/WormNet.v3.benchmark.txt b/examples/algorithms/WormNet.v3.benchmark.txt new file mode 100644 index 00000000..824cfa1c --- /dev/null +++ b/examples/algorithms/WormNet.v3.benchmark.txt @@ -0,0 +1,78736 @@ +C41D11.8 AH9.2 +CD4.2 AH9.2 +K12H4.8 AH9.2 +T07A9.5 AH9.2 +Y113G7A.9 AH9.2 +Y47G6A.8 AH9.2 +Y48B6A.3 AH9.2 +Y56A3A.32 AH9.2 +ZC513.5 B0024.13 +F21F3.5 B0207.12 +K11G12.2 B0207.12 +K11G12.7 B0207.12 +ZC482.1 B0207.12 +C02C6.1 B0207.3 +C09G12.8 B0207.3 +C16A11.1 B0207.3 +C26C6.2 B0207.3 +C33H5.14 B0207.3 +C34D1.3 B0207.3 +C35C5.4 B0207.3 +C38D4.8 B0207.3 +C44F1.5 B0207.3 +C55H1.2 B0207.3 +E02C12.5 B0207.3 +F18E2.5 B0207.3 +F18G5.3 B0207.3 +F22B5.1 B0207.3 +F26H9.6 B0207.3 +F29C12.4 B0207.3 +F38E1.5 B0207.3 +F48C11.1 B0207.3 +F53B1.7 B0207.3 +F56H9.3 B0207.3 +F56H9.4 B0207.3 +K03D3.10 B0207.3 +M01D7.7 B0207.3 +M04C7.1 B0207.3 +R06A10.2 B0207.3 +R07G3.1 B0207.3 +R10H10.5 B0207.3 +T01C2.1 B0207.3 +T07A9.7 B0207.3 +T19C4.6 B0207.3 +W03C9.3 B0207.3 +W03F8.9 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+ZK507.6 ZK1307.6 +ZK792.6 ZK1307.6 +ZK909.2 ZK1307.6 +ZK792.6 ZK507.6 +ZK909.2 ZK507.6 diff --git a/examples/algorithms/plot_betweenness_centrality.py b/examples/algorithms/plot_betweenness_centrality.py new file mode 100644 index 00000000..e8354c66 --- /dev/null +++ b/examples/algorithms/plot_betweenness_centrality.py @@ -0,0 +1,83 @@ +""" +===================== +Betweeness Centrality +===================== + +Betweenness centrality measures of positive gene functional associations +using WormNet v.3-GS. + +Data from: https://www.inetbio.org/wormnet/downloadnetwork.php +""" + +from random import sample +import networkx as nx +import matplotlib.pyplot as plt + +# Gold standard data of positive gene functional associations +# from https://www.inetbio.org/wormnet/downloadnetwork.php +G = nx.read_edgelist("WormNet.v3.benchmark.txt") + +# remove randomly selected nodes (to make example fast) +num_to_remove = int(len(G) / 1.5) +nodes = sample(list(G.nodes), num_to_remove) +G.remove_nodes_from(nodes) + +# remove low-degree nodes +low_degree = [n for n, d in G.degree() if d < 10] +G.remove_nodes_from(low_degree) + +# largest connected component +components = nx.connected_components(G) +largest_component = max(components, key=len) +H = G.subgraph(largest_component) + +# compute centrality +centrality = nx.betweenness_centrality(H, k=10, endpoints=True) + +# compute community structure +lpc = nx.community.label_propagation_communities(H) +community_index = {n: i for i, com in enumerate(lpc) for n in com} + +#### draw graph #### +fig, ax = plt.subplots(figsize=(20, 15)) +pos = nx.spring_layout(H, k=0.15, seed=4572321) +node_color = [community_index[n] for n in H] +node_size = [v * 20000 for v in centrality.values()] +nx.draw_networkx( + H, + pos=pos, + with_labels=False, + node_color=node_color, + node_size=node_size, + edge_color="gainsboro", + alpha=0.4, +) + +# Title/legend +font = {"color": "k", "fontweight": "bold", "fontsize": 20} +ax.set_title("Gene functional association network (C. elegans)", font) +# Change font color for legend +font["color"] = "r" + +ax.text( + 0.80, + 0.10, + "node color = community structure", + horizontalalignment="center", + transform=ax.transAxes, + fontdict=font, +) +ax.text( + 0.80, + 0.06, + "node size = betweeness centrality", + horizontalalignment="center", + transform=ax.transAxes, + fontdict=font, +) + +# Resize figure for label readibility +ax.margins(0.1, 0.05) +fig.tight_layout() +plt.axis("off") +plt.show() |