import math import matplotlib.pyplot as plt import numpy as np from graph_tool.all import * from src import centrality from src import plot from src import fitting def leverage(g, weight): # VertexPropertyMap vp = g.new_vertex_property("double") for v in g.vertices(): li = 0.0 neighbours = g.get_all_neighbours(v) ki = len(neighbours) # sum for nv in neighbours: other_neighbours = g.get_all_neighbours(nv) kj = len(other_neighbours) li += (ki - kj) / (ki + kj) li /= ki vp[v] = li return vp 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): 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 return g, weight points, seed = random_graph() g, weight = spatial_graph(points) g = GraphView(g) # calculate centrality values 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 # normalization min_val, max_val = vp.a.min(), vp.a.max() vp.a = (vp.a - min_val) / (max_val - min_val) # calculate convex hull convex_hull = centrality.convex_hull(g) # plot graph with convex_hull fig = plt.figure(figsize=(15, 5)) ax0, ax1 = fig.subplots(1, 2) plot.graph_plot(fig, ax0, g, vp, convex_hull, f"Random Graph (seed: {seed})") # generate model based on convex hull and associated centrality values quantification = plot.quantification_data(g, vp, convex_hull) # optimize model's piece-wise linear function d = quantification[:, 0] C = quantification[:, 1] m_opt, c0_opt, b_opt, aic_opt = fitting.fit_piece_wise_linear(d, C) # TODO # should this be part of the plotting function itself, it should not be necessary for me to do this d_curve = np.linspace(min(d), max(d), 500) C_curve = np.piecewise( d_curve, [d_curve <= b_opt, d_curve > b_opt], [lambda x: m_opt * x + c0_opt, lambda x: m_opt * b_opt + c0_opt] ) # plot model containing modeled piece-wise linear function plot.quantification_plot(ax1, quantification, d_curve, C_curve, 'Betweenness', aic_opt) # linear regression model m_reg, c0_reg, aic_reg = fitting.fit_linear_regression(d, C) # TODO # should this be part of the plotting function itself, it should not be necessary for me to do this d_curve = np.linspace(min(d), max(d), 500) C_curve = np.piecewise( d_curve, [d_curve >= 0], [lambda x: m_reg * x + c0_reg] ) ax1.plot(d_curve, C_curve, color='k', linewidth=1, label=f"Simple Linear Regression | AIC: {aic_reg}") ax1.legend() fig.savefig(f"model_approximation_betweenness_5000.svg", format='svg')