diff --git a/node_vs_edge_centrality.py b/node_vs_edge_centrality.py new file mode 100644 index 0000000..ddcdc25 --- /dev/null +++ b/node_vs_edge_centrality.py @@ -0,0 +1,139 @@ +import math + +import matplotlib.pyplot as plt +from matplotlib.collections import LineCollection +import matplotlib as mpl +import numpy as np +import squidpy as sq +import scipy +import spatialdata as sd +from spatialdata_io.experimental import to_legacy_anndata +from graph_tool.all import * + +from src import centrality +from src import plot +from src import fitting + + +def merfish(): + """ + Merfish dataset from `squidpy`. + """ + adata = sq.datasets.merfish() + adata = adata[adata.obs.Bregma == -9].copy() + return adata + + +def random_graph(n=5000, seed=None): + """ + Uniformly random point cloud generation. + `n` [int] Number of points to generate. Default 5000 seems like a good starting point in point density and corresponding runtime for the subsequent calculations. + @return [numpy.ndarray] Array of shape(n, 2) containing the coordinates for each point of the generated point cloud. + """ + if seed is None: + import secrets + seed = secrets.randbits(128) + rng = np.random.default_rng(seed=seed) + return rng.random((n, 2)), seed + + +def spatial_graph(adata): + """ + Generate the spatial graph using delaunay for the given `adata`. + `adata` will contain the calculated spatial graph contents in the keys + adata.obsm['spatial']` in case the `adata` is created from a dataset of *squidpy*. + @return [Graph] generated networkx graph from adata.obsp['spatial_distances'] + """ + g, pos = graph_tool.generation.triangulation(adata, type="delaunay") + g.vp["pos"] = pos + weight = g.new_edge_property("double") + for e in g.edges(): + weight[e] = math.sqrt(sum(map(abs, pos[e.source()].a - pos[e.target()].a)))**2 + g.ep["weight"] = weight + return g, weight + + +def plot_graph_edges(g, centralities, fig, ax, name): + pos = g.vp["pos"] + + norm = mpl.colors.Normalize(vmin=centralities.min(), vmax=centralities.max()) + cmap = plt.cm.plasma.resampled(g.num_edges()) + for idx, e in enumerate(g.edges()): + ex = [pos[e.source()][0], pos[e.target()][0]] + ey = [pos[e.source()][1], pos[e.target()][1]] + ax.add_collection(LineCollection([np.column_stack([ex, ey])], colors=cmap(norm(centralities[idx])), linewidths=0.5)) + + ax.set_title(name) + fig.colorbar(plt.cm.ScalarMappable(norm=norm, cmap=cmap), ax=ax) + + +def plot_graph_nodes(g, centralities, fig, ax, name): + pos = g.vp["pos"] + x = [] + y = [] + for v in g.vertices(): + ver = pos[v] + x.append(ver[0]) + y.append(ver[1]) + + sc = ax.scatter(x, y, s=1, c=centralities, cmap=plt.cm.plasma) + ax.set_title(name) + fig.colorbar(sc, ax=ax) + + +def plot_relationship_nodes(g, vp, convex_hull, fig, ax, name): + quantification = plot.quantification_data(g, vp, convex_hull) + + ax.set_title(name) + ax.set_xlabel('Distance to Bounding-Box') + ax.set_ylabel('Centrality') + ax.scatter(quantification[:, 0], quantification[:, 1], c=quantification[:, 1], cmap=plt.cm.plasma, s=0.2) + + +def plot_relationship_edges(g, ep, convex_hull, fig, ax, name): + quantification = plot.quantification_data_edges(g, ep, convex_hull) + + ax.set_title(name) + ax.set_xlabel('Distance to Bounding-Box') + ax.set_ylabel('Centrality') + ax.scatter(quantification[:, 0], quantification[:, 1], c=quantification[:, 1], cmap=plt.cm.plasma, s=0.2) + + +# points, seed = random_graph(n=3000) +# g, weight = spatial_graph(points) +adata = merfish() +g, weight = spatial_graph(adata.obsm['spatial']) +g = GraphView(g) + +# plot graph +fig = plt.figure(figsize=(15, 18), layout='constrained') +fig.suptitle(f"Merfish", fontsize=16) +row1, row2, row3 = fig.subplots(3, 2) + +ax1, ax2 = row1 +ax3, ax4 = row2 +ax5, ax6 = row3 + +# relationship with betweenness scoring for both node and edges +vp, ep = betweenness(g, weight=weight) +vp.a = np.nan_to_num(vp.a) # correct floating point values +ep.a = np.nan_to_num(ep.a) # correct floating point values + +# compare location of centrality scores +plot_graph_nodes(g, vp.a, fig, ax1, "Node Betweenness centrality") +plot_graph_edges(g, ep.a, fig, ax2, "Edge Betweenness centrality") + +# compare relative amount of centrality scores +ax3.hist(vp.a, bins=50) +ax3.set_xlabel('Centrality scorce') +ax3.set_ylabel('# Occurances') +ax4.hist(ep.a, bins=50) +ax4.set_xlabel('Centrality scorce') +ax4.set_ylabel('# Occurances') + +# compare relationships +convex_hull = centrality.convex_hull(g) +plot_relationship_nodes(g, vp, convex_hull, fig, ax5, "Node Betweenness relationship") +plot_relationship_edges(g, ep, convex_hull, fig, ax6, "Node Betweenness relationship") + +fig.savefig(f"node_vs_edge_betweenness_centrality_merfish.pdf", format='pdf')