pull request fixes

nwlandry · Jan 30, 2024 · 4151fcf · 4151fcf
1 parent 744dfae
commit 4151fcf
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Showing 5 changed files with 1,103 additions and 63 deletions.
diff --git a/Extra/plot_fig1.ipynb b/Extra/plot_fig1.ipynb
diff --git a/Extra/plot_fig2.ipynb b/Extra/plot_fig2.ipynb
diff --git a/fig_settings.py b/fig_settings.py
@@ -6,22 +6,13 @@
 """
 
 import os
-
 import matplotlib.pylab as pylab
 import matplotlib.pyplot as plt
-
-
 import matplotlib as mpl
-import matplotlib.colors as mcolors
-from cycler import cycler
 import cmasher as cmr
 
-
-
 
 #color styling
-
-
 def set_colors(n_colors = 2):
     global cmap 
     global pallette
@@ -32,9 +23,6 @@ def set_colors(n_colors = 2):
     mpl.rcParams['axes.prop_cycle'] = mpl.cycler(color= pallette)
 
 
-# cmap = mcolors.LinearSegmentedColormap.from_list('my_cmap',[pallete[0],pallete[1]])
-# cmap = cmr.ember
-
 def set_fontsize():
     plt.rcParams['axes.labelsize'] = 30
     # Set the global default size of the tick labels
@@ -86,11 +74,6 @@ def fig_size(frac_width, frac_height, n_cols=1, n_rows=1):
 
     return (width, height)
 
-
-
-
-
-
 def get_formats():
     return ["eps", "jpg", "pdf", "png", "tif"]
 

diff --git a/plot_fig1.py b/plot_fig1.py
@@ -1,21 +1,13 @@
 
 import json
-
 import arviz as az
-import cmasher as cmr
-import matplotlib.cm as cm
 import matplotlib.pyplot as plt
 import numpy as np
 import seaborn as sns
 import xgi
-
 import fig_settings as fs
 from lcs import *
 
-import matplotlib as mpl
-import matplotlib.colors as mcolors
-from cycler import cycler
-
 
 
 fs.set_fonts()
@@ -45,7 +37,7 @@
 
 x = contagion_process(A, gamma, c, x0, tmin=0, tmax=100, random_seed=2)
 
-infected_color = 'C1' 
+infected_color = 'C0' 
 susceptible_color = "white"
 subgraph_color = "black"
 graph_color = (0.1, 0.1, 0.1, 0.1)
@@ -59,7 +51,7 @@
 pos = xgi.pca_transform(xgi.pairwise_spring_layout(H, seed=5, k=0.3))
 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'
+node_fc[12] = 'C1'
 
 dyad_color = [subgraph_color if e in sg else graph_color for e in H.edges]
 
@@ -76,9 +68,6 @@
     ax = ax1
 )
 
-# plt.savefig("Figures/Fig1/zkc_network.svg", dpi=1000)
-# plt.savefig("Figures/Fig1/zkc_network.png", dpi=1000)
-
 
 """
 Panel 2: 
@@ -101,9 +90,6 @@
 l1 = np.array(data["l1"], dtype=float)
 l2 = np.array(data["l2"], dtype=float)
 
-# import cmasher as cmr
-# cmap = cmr.ember
-
 kmax = np.max(degrees(A))
 n = A.shape[0]
 
@@ -112,7 +98,6 @@
 # simple contagion
 c1_mean = c1_samples.mean(axis=0)
 ax2.plot(nus, c1, "-", color='C0', label="Simple contagion")
-# ax2.scatter(nus, c1_mean, linewidth=0.5, color=colors[2])
 
 err_c1 = np.zeros((2, n))
 c1_mode = np.zeros(n)
@@ -126,7 +111,6 @@
 # threshold contagion, tau=2
 c2_mean = c2_samples.mean(axis=0)
 ax2.plot(nus, c2, "-", color='C1', label="Complex contagion")
-# ax2.scatter(nus, c2_mean, linewidth=0.5, color=colors[1])
 
 err_c2 = np.zeros((2, n))
 c2_mode = np.zeros(n)
@@ -150,10 +134,6 @@
 sns.despine()
 
 
-# # ax2.savefig("Figures/Fig1/zkc_infer_contagion_function.svg", dpi=1000)
-# # ax2.savefig("Figures/Fig1/zkc_infer_contagion_function.png", dpi=1000)
-# ax2.show()
-
 with open("Data/zkc_infer_vs_tmax.json") as file:
     data = json.load(file)
 
@@ -164,7 +144,6 @@
 fce = np.array(data["fce"], dtype=float)
 
 
-#ax3.semilogx(tmax, sps[0].mean(axis=1), color=colors[2], label="Simple contagion")
 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.fill_between(
@@ -197,7 +176,6 @@
 sps = np.array(data["sps"], dtype=float)
 fce = np.array(data["fce"], dtype=float)
 
-#cmap = cmr.gem
 cmap = cmap
 
 sps_summary = sps.mean(axis=2)
@@ -222,8 +200,5 @@
 cbar = plt.colorbar(c, cax=cbar_ax)
 cbar.set_label(r"F-Score", fontsize=12, rotation=270, labelpad=15)
 
-#plt.tight_layout()
-
-
 plt.savefig("Figures/Fig1/figure1_4panel.png", dpi=1000)
 plt.savefig("Figures/Fig1/figure1_4_panel.pdf", dpi=1000)
diff --git a/plot_fig2.py b/plot_fig2.py
@@ -1,29 +1,17 @@
 
 import json
 
-import arviz as az
-import cmasher as cmr
-import matplotlib.cm as cm
 import matplotlib.pyplot as plt
 import numpy as np
-import seaborn as sns
 import xgi
 
 import fig_settings as fs
 from lcs import *
 
-import matplotlib as mpl
-import matplotlib.colors as mcolors
-from cycler import cycler
-
-
-
 fs.set_fonts()
 fs.set_colors()
-#fs.set_fontsize()
-cmap = fs.cmap
-
 fs.set_fonts({"font.family": "sans-serif"})
+cmap = fs.cmap
 
 
 models = ["Erdos-Renyi", "SBM", "Watts-Strogatz", "CM", "clustered_network"]
@@ -51,7 +39,6 @@
 ]
 convert_to_log = [False, False, True, False, False]
 
-
 def visualize_networks(i, ax):
     n = 50
     match i:
@@ -90,11 +77,6 @@ def visualize_networks(i, ax):
         case 2:
             pos = xgi.circular_layout(H)
         case 3:
-            # sorted_nodes = [n for n, _ in sorted(H.nodes.degree.asdict().items(), key=lambda d: d[1])]
-            # Hnew = xgi.Hypergraph()
-            # Hnew.add_nodes_from(sorted_nodes)
-            # Hnew.add_edges_from(e)
-            # pos = xgi.circular_layout(Hnew)
             pos = xgi.pairwise_spring_layout(H, seed=2)
         case 4:
             pos = xgi.pairwise_spring_layout(H, seed=2)