updated legends for different graphs
This commit is contained in:
Luis Aleixo
parent
90ae11ebc4
commit
3724009060
1 changed files with 109 additions and 76 deletions
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@ -82,8 +82,40 @@ def exposure_model_from_vl_talking(viral_loads):
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upper_percentiles.append(np.quantile(emission_rate, 0.99))
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# divide by 4 to have in 15min (quarter of an hour)
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build_plot(viral_loads, er_means,
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lower_percentiles, upper_percentiles, coleman_etal_vl_talking, [x/4 for x in coleman_etal_er_talking])
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coleman_etal_er_talking_2 = [x/4 for x in coleman_etal_er_talking]
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ax.plot(viral_loads, er_means)
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ax.fill_between(viral_loads, lower_percentiles,
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upper_percentiles, alpha=0.2)
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ax.set_yscale('log')
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############# Coleman #############
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plt.scatter(coleman_etal_vl_talking, coleman_etal_er_talking_2, marker='x')
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x_hull, y_hull = get_enclosure_points(
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coleman_etal_vl_talking, coleman_etal_er_talking_2)
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# plot shape
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plt.fill(x_hull, y_hull, '--', c='orange', alpha=0.2)
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############# Markers #############
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markers = [5, 'd', 4]
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############ Legend ############
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result_from_model = mlines.Line2D(
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[], [], color='blue', marker='_', linestyle='None')
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coleman = mlines.Line2D([], [], color='orange',
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marker='x', linestyle='None')
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title_proxy = Rectangle((0, 0), 0, 0, color='w')
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titles = ["$\\bf{CARA \, \\it{(SARS-CoV-2)}:}$", "$\\bf{Coleman \, et \, al. \, \\it{(SARS-CoV-2)}:}$"]
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leg = plt.legend([title_proxy, result_from_model, title_proxy, coleman],
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[titles[0], "Result from model", titles[1], "Dataset"])
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# Move titles to the left
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for item, label in zip(leg.legendHandles, leg.texts):
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if label._text in titles:
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width = item.get_window_extent(fig.canvas.get_renderer()).width
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label.set_ha('left')
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label.set_position((-3*width, 0))
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############ Plot ############
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plt.title('Exhaled virions while talking for 15min',
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@ -129,15 +161,87 @@ def exposure_model_from_vl_breathing(viral_loads):
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)
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exposure_model = exposure_mc.build_model(size=SAMPLE_SIZE)
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# divide by 2 to have in 30min (half an hour)
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emission_rate = exposure_model.concentration_model.infected.emission_rate_when_present() /2
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emission_rate = exposure_model.concentration_model.infected.emission_rate_when_present() / 2
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er_means.append(np.mean(emission_rate))
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er_medians.append(np.median(emission_rate))
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lower_percentiles.append(np.quantile(emission_rate, 0.01))
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upper_percentiles.append(np.quantile(emission_rate, 0.99))
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# divide by 2 to have in 30min (half an hour)
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build_plot(viral_loads, er_means,
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lower_percentiles, upper_percentiles, coleman_etal_vl_breathing, [x/2 for x in coleman_etal_er_breathing], milton_vl, [x/2 for x in milton_er], yann_vl, [x/2 for x in yann_er])
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coleman_etal_er_breathing_2 = [x/2 for x in coleman_etal_er_breathing]
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milton_er_2 = [x/2 for x in milton_er]
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yann_er_2 = [x/2 for x in yann_er]
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ax.plot(viral_loads, er_means)
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ax.fill_between(viral_loads, lower_percentiles,
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upper_percentiles, alpha=0.2)
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ax.set_yscale('log')
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############# Coleman #############
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plt.scatter(coleman_etal_vl_breathing,
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coleman_etal_er_breathing_2, marker='x')
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x_hull, y_hull = get_enclosure_points(
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coleman_etal_vl_breathing, coleman_etal_er_breathing_2)
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# plot shape
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plt.fill(x_hull, y_hull, '--', c='orange', alpha=0.2)
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############# Markers #############
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markers = [5, 'd', 4]
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############# Milton et al #############
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try:
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for index, m in enumerate(markers):
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plt.scatter(milton_vl[index], milton_er_2[index],
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marker=m, color='red')
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x_hull, y_hull = get_enclosure_points(milton_vl, milton_er_2)
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# plot shape
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plt.fill(x_hull, y_hull, '--', c='red', alpha=0.2)
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except:
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print("No data for Milton et al")
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############# Yan et al #############
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try:
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plt.scatter(yann_vl[0], yann_er_2[0], marker=markers[0], color='green')
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plt.scatter(yann_vl[1], yann_er_2[1],
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marker=markers[1], color='green', s=50)
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plt.scatter(yann_vl[2], yann_er_2[2], marker=markers[2], color='green')
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x_hull, y_hull = get_enclosure_points(yann_vl, yann_er_2)
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# plot shape
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plt.fill(x_hull, y_hull, '--', c='green', alpha=0.2)
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except:
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print("No data for Yan et al")
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############ Legend ############
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result_from_model = mlines.Line2D(
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[], [], color='blue', marker='_', linestyle='None')
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coleman = mlines.Line2D([], [], color='orange',
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marker='x', linestyle='None')
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milton_mean = mlines.Line2D(
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[], [], color='red', marker='d', linestyle='None') # mean
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milton_25 = mlines.Line2D(
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[], [], color='red', marker=5, linestyle='None') # 25
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milton_75 = mlines.Line2D(
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[], [], color='red', marker=4, linestyle='None') # 75
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yann_mean = mlines.Line2D([], [], color='green',
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marker='d', linestyle='None') # mean
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yann_25 = mlines.Line2D([], [], color='green',
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marker=5, linestyle='None') # 25
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yann_75 = mlines.Line2D([], [], color='green',
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marker=4, linestyle='None') # 75
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title_proxy = Rectangle((0, 0), 0, 0, color='w')
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titles = ["$\\bf{CARA \, \\it{(SARS-CoV-2)}:}$", "$\\bf{Coleman \, et \, al. \, \\it{(SARS-CoV-2)}:}$",
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"$\\bf{Milton \, et \, al. \,\\it{(Influenza)}:}$", "$\\bf{Yann \, et \, al. \,\\it{(Influenza)}:}$"]
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leg = plt.legend([title_proxy, result_from_model, title_proxy, coleman, title_proxy, milton_mean, milton_25, milton_75, title_proxy, yann_mean, yann_25, yann_75],
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[titles[0], "Result from model", titles[1], "Dataset", titles[2], "Mean", "25th per.", "75th per.", titles[3], "Mean", "25th per.", "75th per."])
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# Move titles to the left
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for item, label in zip(leg.legendHandles, leg.texts):
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if label._text in titles:
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width = item.get_window_extent(fig.canvas.get_renderer()).width
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label.set_ha('left')
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label.set_position((-3*width, 0))
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############ Plot ############
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plt.title('Exhaled virions while breathing for 30 min',
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@ -169,77 +273,6 @@ def get_enclosure_points(x_coordinates, y_coordinates):
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return x_hull, y_hull
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def build_legend(fig):
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result_from_model = mlines.Line2D(
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[], [], color='blue', marker='_', linestyle='None')
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coleman = mlines.Line2D([], [], color='orange',
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marker='x', linestyle='None')
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milton_mean = mlines.Line2D(
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[], [], color='red', marker='d', linestyle='None') # mean
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milton_25 = mlines.Line2D(
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[], [], color='red', marker=5, linestyle='None') # 25
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milton_75 = mlines.Line2D(
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[], [], color='red', marker=4, linestyle='None') # 75
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yann_mean = mlines.Line2D([], [], color='green',
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marker='d', linestyle='None') # mean
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yann_25 = mlines.Line2D([], [], color='green',
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marker=5, linestyle='None') # 25
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yann_75 = mlines.Line2D([], [], color='green',
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marker=4, linestyle='None') # 75
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title_proxy = Rectangle((0, 0), 0, 0, color='w')
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titles = ["$\\bf{CARA \, \\it{(SARS-CoV-2)}:}$", "$\\bf{Coleman \, et \, al. \, \\it{(SARS-CoV-2)}:}$",
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"$\\bf{Milton \, et \, al. \,\\it{(Influenza)}:}$", "$\\bf{Yann \, et \, al. \,\\it{(Influenza)}:}$"]
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leg = plt.legend([title_proxy, result_from_model, title_proxy, coleman, title_proxy, milton_mean, milton_25, milton_75, title_proxy, yann_mean, yann_25, yann_75],
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[titles[0], "Result from model", titles[1], "Dataset", titles[2], "Mean", "25th per.", "75th per.", titles[3], "Mean", "25th per.", "75th per."])
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# Move titles to the left
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for item, label in zip(leg.legendHandles, leg.texts):
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if label._text in titles:
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width = item.get_window_extent(fig.canvas.get_renderer()).width
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label.set_ha('left')
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label.set_position((-3*width, 0))
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def build_plot(viral_loads, er_means, lower_percentiles, upper_percentiles, coleman_etal_vl, coleman_etal_er, milton_vl, milton_er, yann_vl, yann_er, ):
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ax.plot(viral_loads, er_means)
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ax.fill_between(viral_loads, lower_percentiles,
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upper_percentiles, alpha=0.2)
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ax.set_yscale('log')
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############# Coleman #############
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plt.scatter(coleman_etal_vl, coleman_etal_er, marker='x')
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x_hull, y_hull = get_enclosure_points(
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coleman_etal_vl, coleman_etal_er)
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# plot shape
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plt.fill(x_hull, y_hull, '--', c='orange', alpha=0.2)
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############# Markers #############
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markers = [5, 'd', 4]
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############# Milton et al #############
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for index, m in enumerate(markers):
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plt.scatter(milton_vl[index], milton_er[index],
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marker=m, color='red')
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x_hull, y_hull = get_enclosure_points(milton_vl, milton_er)
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# plot shape
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plt.fill(x_hull, y_hull, '--', c='red', alpha=0.2)
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############# Yan et al #############
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plt.scatter(yann_vl[0], yann_er[0], marker=markers[0], color='green')
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plt.scatter(yann_vl[1], yann_er[1], marker=markers[1], color='green', s=50)
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plt.scatter(yann_vl[2], yann_er[2], marker=markers[2], color='green')
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x_hull, y_hull = get_enclosure_points(yann_vl, yann_er)
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# plot shape
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plt.fill(x_hull, y_hull, '--', c='green', alpha=0.2)
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############ Legend ############
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build_legend(fig)
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return plt
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# # Milton
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# boxes = [
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# {
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