Fig 1 updates (#31)

* Fig 1 updates * Fixed bugs found by nicholas + adjust fonts and sizing a bit more * simplify code --------- Co-authored-by: Nicholas Landry <[email protected]>
nwlandry · Apr 16, 2024 · 253d5af · 253d5af
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diff --git a/Figures/Fig1/fig1.pdf b/Figures/Fig1/fig1.pdf
diff --git a/Figures/Fig1/fig1.png b/Figures/Fig1/fig1.png
diff --git a/fig_settings.py b/fig_settings.py
@@ -23,15 +23,15 @@ def set_colors(n_colors=2):
 
 def set_fonts(extra_params={}):
     params = {
-        "font.family": "Sans-Serif",
-        "font.sans-serif": ["Tahoma", "DejaVu Sans", "Lucida Grande", "Verdana"],
+        "font.family": "Serif",
+        # "font.sans-serif": ["Tahoma", "DejaVu Sans", "Lucida Grande", "Verdana"],
         "mathtext.fontset": "cm",
         "legend.fontsize": 12,
-        "axes.labelsize": 15,
-        "axes.titlesize": 15,
-        "xtick.labelsize": 15,
-        "ytick.labelsize": 15,
-        "figure.titlesize": 15,
+        "axes.labelsize": 12,
+        "axes.titlesize": 12,
+        "xtick.labelsize": 12,
+        "ytick.labelsize": 12,
+        "figure.titlesize": 12,
     }
     for key, value in extra_params.items():
         params[key] = value

diff --git a/plot_fig1.py b/plot_fig1.py
@@ -10,11 +10,11 @@
 import fig_settings as fs
 from lcs import *
 
-axislabel_fontsize = 20
-tick_fontsize = 18
+axislabel_fontsize = 12
+tick_fontsize = 12
 fs.set_fonts(
     {
-        "font.family": "sans-serif",
+        "font.family": "serif",
         "axes.labelsize": axislabel_fontsize,
         "xtick.labelsize": tick_fontsize,
         "ytick.labelsize": tick_fontsize,
@@ -23,16 +23,18 @@
 fs.set_colors()
 cmap = fs.cmap
 
-fig = plt.figure(figsize=(8, 6))
-plt.subplots_adjust(left=0.1, right=0.86, bottom=0.15, top=0.95, wspace=0.4, hspace=0.4)
+fig = plt.figure(figsize=(5.5, 5))
+plt.subplots_adjust(left=0.12, right=0.89, bottom=0.15, top=0.95)
 
-gs = GridSpec(2, 2, hspace=0.4, wspace=0.4)
+gs = GridSpec(2, 2, hspace=0.6, wspace=0.5)
 
 """
 Panel 1: Network Viz
 """
 ax1 = fig.add_subplot(gs[0])
 
+ax1.text(-0.36, 1.05, "(a)", transform=ax1.transAxes, fontsize=13, fontweight='bold', va="top")
+
 el = zkc(format="edgelist")
 H = xgi.Hypergraph(el)
 A = zkc()
@@ -53,15 +55,17 @@
 infected_color = "C1"
 susceptible_color = "white"
 subgraph_color = "black"
-graph_color = (0.1, 0.1, 0.1, 0.1)
+graph_color = (0.7, 0.7, 0.7, 0.5)
 subgraph_node_lc = "black"
 graph_node_lc = (0.3, 0.3, 0.3)
 
 sg = H.nodes.memberships(i)
 nbrs = H.nodes.neighbors(i)
 nbrs.add(i)
 
-pos = xgi.pca_transform(xgi.pairwise_spring_layout(H, seed=5, k=0.3))
+# rotate pos by 30 degrees
+pos = xgi.pca_transform(xgi.pairwise_spring_layout(H, seed=5, k=0.25), theta=30)
+
 node_fc = [infected_color if x[t, i] else susceptible_color for i in H.nodes]
 node_ec = [subgraph_node_lc if n in nbrs else graph_node_lc for n in H.nodes]
 node_fc[12] = "C0"
@@ -75,17 +79,22 @@
     node_size=6.5,
     node_fc=node_fc,
     dyad_color=dyad_color,
-    dyad_lw=0.5,
+    dyad_lw=0.8,
     node_ec=node_ec,
-    node_lw=0.5,
-    ax=ax1,
+    node_lw=0.8,
+    ax=ax1
 )
+plt.scatter(pos[13][0], pos[13][1], s=50, c='C0', edgecolors='black', linewidths=0.8, zorder=10, marker='s')
+
+ax1.set_xlim([1.1 * min([pos[i][0] for i in pos]), 1.1 * max([pos[i][0] for i in pos])])
 
 
 """
 Panel 2: 
 """
 ax2 = fig.add_subplot(gs[1])
+ax2.text(-0.39, 1.05, "(b)", transform=ax2.transAxes, fontsize=12, fontweight='bold',  va="top")
+
 
 with open("Data/zkc_infer_contagion_functions.json") as file:
     data = json.load(file)
@@ -110,7 +119,7 @@
 
 # simple contagion
 c1_mean = c1_samples.mean(axis=0)
-ax2.plot(nus, c1, "-", color="C0", label="Simple contagion")
+ax2.plot(nus, c1, "-", color="C0", lw=5, alpha=0.5)
 
 err_c1 = np.zeros((2, n))
 c1_mode = np.zeros(n)
@@ -119,11 +128,15 @@
     x, y = interval
     err_c1[0, i] = max(c1_mean[i] - x, 0)
     err_c1[1, i] = max(y - c1_mean[i], 0)
-ax2.errorbar(nus, c1_mean, err_c1, color="C0", fmt="o")
+
+
+offset_distance = 0.15
+ax2.errorbar(nus - offset_distance, c1_mean, err_c1, color="C0", fmt="o",
+             capsize=3, markersize=5, markeredgecolor="#315b7d", label="Simple")
 
 # threshold contagion, tau=2
 c2_mean = c2_samples.mean(axis=0)
-ax2.plot(nus, c2, "-", color="C1", label="Complex contagion")
+ax2.plot(nus, c2, "-", color="C1", lw=5, alpha=0.5)
 
 err_c2 = np.zeros((2, n))
 c2_mode = np.zeros(n)
@@ -132,24 +145,28 @@
     x, y = interval
     err_c2[0, i] = max(c2_mean[i] - x, 0)
     err_c2[1, i] = max(y - c2_mean[i], 0)
-ax2.errorbar(nus, c2_mean, err_c2, color="C1", fmt="o")
+ax2.errorbar(nus + offset_distance, c2_mean, err_c2, color="C1", fmt="o",
+             capsize=3, markersize=5, markeredgecolor="#391c23", label="Complex")
+
 
 ax2.set_xticks(np.arange(0, n, 5))
-ax2.set_xlabel(r"$\nu$")
-ax2.set_ylabel(r"$c(\nu)$")
+ax2.set_xlabel(r"# of infected neighbors, $\nu$")
+ax2.set_ylabel(r"Probability, $c(\nu)$")
 
-ax2.set_xlim([0, kmax + 2.5])
+ax2.set_xlim([0, 13.5])
 ax2.set_ylim([0, 1])
 ax2.set_yticks([0, 0.5, 1], [0, 0.5, 1])
 
-ax2.legend(loc="upper left")
+ax2.legend(loc='upper left', bbox_to_anchor=(-0.1, 0.9, 0.2, 0.2), 
+           handletextpad=0.1, frameon=False)
 
 sns.despine()
 
 """"
 Panel 3: recovery vs. tmax
 """
 ax3 = fig.add_subplot(gs[2])
+ax3.text(-0.35, 1.05, "(c)", transform=ax3.transAxes, fontsize=12, fontweight='bold',  va="top")
 
 
 with open("Data/zkc_infer_vs_tmax.json") as file:
@@ -162,21 +179,23 @@
 fce = np.array(data["fce"], dtype=float)
 
 
-ax3.semilogx(tmax, sps[0].mean(axis=1), color="C0", label="Simple contagion")
-ax3.semilogx(tmax, sps[1].mean(axis=1), color="C1", label="Complex contagion")
+ax3.semilogx(tmax, sps[0].mean(axis=1), color="C0", label="Simple")
+ax3.semilogx(tmax, sps[1].mean(axis=1), color="C1", label="Complex")
 ax3.fill_between(
     tmax,
     sps[0].mean(axis=1) - sps[0].std(axis=1),
     sps[0].mean(axis=1) + sps[0].std(axis=1),
     alpha=0.3,
     color="C0",
+    edgecolor="none"
 )
 ax3.fill_between(
     tmax,
     sps[1].mean(axis=1) - sps[1].std(axis=1),
     sps[1].mean(axis=1) + sps[1].std(axis=1),
     alpha=0.3,
     color="C1",
+    edgecolor="none"
 )
 ax3.set_ylabel("Performance")
 ax3.set_xlabel(r"$t_{max}$")
@@ -188,13 +207,15 @@
 ax3.set_ylim([0, 1])
 ax3.set_yticks([0, 0.5, 1], [0, 0.5, 1])
 
-ax3.legend(loc="upper left")
+ax3.legend(loc="lower right",   bbox_to_anchor=(0.85, 0, 0.2, 0.2), 
+           markerfirst=False, frameon=False, handlelength=0.8)
 sns.despine()
 
 """
 Panel 4: heatmap of recover vs. beta and f
 """
 ax4 = fig.add_subplot(gs[3])
+ax4.text(-0.38, 1.05, "(d)", transform=ax4.transAxes, fontsize=12, fontweight='bold',  va="top")
 
 with open("Data/zkc_frac_vs_beta.json") as file:
     data = json.load(file)
@@ -210,24 +231,24 @@
 
 
 c = ax4.imshow(
-    to_imshow_orientation(sps_summary),
-    extent=(min(frac), max(frac), min(beta), max(beta)),
+    np.fliplr(to_imshow_orientation(sps_summary)),
+    extent=(min(frac), max(frac), max(beta), min(beta)),
     aspect="auto",
     cmap=cmap,
     vmin=0,
     vmax=1,
 )
-ax4.set_xlabel(r"$f$")
-ax4.set_ylabel(r"$\beta$")
+ax4.set_xlabel(r"Complexity, $\lambda$")
+ax4.set_ylabel(r"Infectivity, $\beta$")
 
 ax4.set_xticks([0, 0.5, 1], [0, 0.5, 1])
 ax4.set_yticks([0, 0.5, 1], [0, 0.5, 1])
 
 
-cbar_ax = fig.add_axes([0.875, 0.15, 0.015, 0.335])  # x, y, width, height
+cbar_ax = fig.add_axes([0.91, 0.15, 0.015, 0.31])  # x, y, width, height
 cbar = plt.colorbar(c, cax=cbar_ax)
-cbar.set_label(r"Performance", fontsize=axislabel_fontsize, rotation=270, labelpad=25)
-cbar_ax.set_yticks([0, 0.5, 1], [0, 0.5, 1], fontsize=tick_fontsize)
+cbar.set_label(r"Performance", fontsize=axislabel_fontsize, rotation=270, labelpad=10)
+cbar_ax.set_yticks([0, 1], [0, 1], fontsize=tick_fontsize)
 
 plt.savefig("Figures/Fig1/fig1.png", dpi=1000)
 plt.savefig("Figures/Fig1/fig1.pdf", dpi=1000)