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Legends and colormap

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This commit is contained in:
Luis Aleixo 2021-09-03 11:16:21 +02:00
parent 32a2a75bc9
commit 7be638c92f
1 changed files with 48 additions and 15 deletions
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63
cara/model_scenarios.py
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@ -437,17 +437,21 @@ def exposure_model_from_vl_breathing(viral_loads):
def exposure_model_from_vl_breathing_cn(viral_loads):
n_lines = 5
min_val, max_val = 0.25,0.85
n = 10
orig_cmap = plt.cm.Blues
colors = orig_cmap(np.linspace(min_val, max_val, n))
n_lines = 30
cns = np.linspace(0.01, 0.5, n_lines)
norm = mpl.colors.Normalize(vmin=cns.min(), vmax=cns.max())
cmap = mpl.cm.ScalarMappable(norm=norm, cmap=mpl.cm.Blues)
cmap = mpl.cm.ScalarMappable(norm=norm, cmap=mpl.colors.LinearSegmentedColormap.from_list("mycmap", colors))
cmap.set_array([])
for cn in tqdm(cns):
er_means = []
er_medians = []
lower_percentiles = []
upper_percentiles = []
for vl in viral_loads:
exposure_mc = mc.ExposureModel(
concentration_model=mc.ConcentrationModel(
@ -479,25 +483,54 @@ def exposure_model_from_vl_breathing_cn(viral_loads):
# divide by 2 to have in 30min (half an hour)
emission_rate = exposure_model.concentration_model.infected.emission_rate_when_present(cn_B = cn, cn_L = 1.0) / 2
er_means.append(np.mean(emission_rate))
er_medians.append(np.median(emission_rate))
lower_percentiles.append(np.quantile(emission_rate, 0.01))
upper_percentiles.append(np.quantile(emission_rate, 0.99))
# divide by 2 to have in 30min (half an hour)
coleman_etal_er_breathing_2 = [x/2 for x in coleman_etal_er_breathing]
milton_er_2 = [x/2 for x in milton_er]
yann_er_2 = [x/2 for x in yann_er]
ax.plot(viral_loads, er_means, color=cmap.to_rgba(cn), linewidth=1)
ax.plot(viral_loads, er_means, color=cmap.to_rgba(cn, alpha=0.75), linewidth=0.5)
#ax.fill_between(viral_loads, lower_percentiles,
# upper_percentiles, alpha=0.2)
fig.colorbar(cmap, ticks=cns)
er_means = []
for vl in viral_loads:
exposure_mc = mc.ExposureModel(
concentration_model=mc.ConcentrationModel(
room=models.Room(volume=100, humidity=0.5),
ventilation=models.AirChange(
active=models.SpecificInterval(((0, 24),)),
air_exch=0.25,
),
infected=mc.InfectedPopulation(
number=1,
virus=models.Virus(
viral_load_in_sputum=10**vl,
infectious_dose=50.,
),
presence=mc.SpecificInterval(((0, 2),)),
mask=models.Mask.types["No mask"],
activity=activity_distributions['Seated'],
expiration=models.Expiration.types['Breathing'],
),
),
exposed=mc.Population(
number=14,
presence=mc.SpecificInterval(((0, 2),)),
activity=models.Activity.types['Seated'],
mask=models.Mask.types["No mask"],
),
)
exposure_model = exposure_mc.build_model(size=SAMPLE_SIZE)
# divide by 2 to have in 30min (half an hour)
emission_rate = exposure_model.concentration_model.infected.emission_rate_when_present(cn_B = 0.1, cn_L = 1.0) / 2
er_means.append(np.mean(emission_rate))
ax.plot(viral_loads, er_means, color=cmap.to_rgba(cn, alpha=0.75), linewidth=1, ls='--')
plt.text(viral_loads[int(len(viral_loads)*0.95)], er_means[-1], "cn_B=0.1", color='black', size='small')
fig.colorbar(cmap, ticks=[0.01, 0.25, 0.5], label="Particle emission concentration for breathing.")
ax.set_yscale('log')
############# Coleman #############
plt.scatter(coleman_etal_vl_breathing,
coleman_etal_er_breathing_2, marker='x')
coleman_etal_er_breathing_2, marker='x', c='orange')
x_hull, y_hull = get_enclosure_points(
coleman_etal_vl_breathing, coleman_etal_er_breathing_2)
# plot shape
@ -552,7 +585,7 @@ def exposure_model_from_vl_breathing_cn(viral_loads):
titles = ["$\\bf{CARA \, \\it{(SARS-CoV-2)}:}$", "$\\bf{Coleman \, et \, al. \, \\it{(SARS-CoV-2)}:}$",
"$\\bf{Milton \, et \, al. \,\\it{(Influenza)}:}$", "$\\bf{Yann \, et \, al. \,\\it{(Influenza)}:}$"]
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],
[titles[0], "Result from model", titles[1], "Dataset", titles[2], "Mean", "25th per.", "75th per.", titles[3], "Mean", "25th per.", "75th per."])
[titles[0], "Results from model", titles[1], "Dataset", titles[2], "Mean", "25th per.", "75th per.", titles[3], "Mean", "25th per.", "75th per."])
# Move titles to the left
for item, label in zip(leg.legendHandles, leg.texts):