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plot with log scale on y axis

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This commit is contained in:
Luis Aleixo 2021-08-05 13:40:57 +02:00
parent ae085826dd
commit 90040a62a2
1 changed files with 23 additions and 14 deletions
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37
cara/apps/calculator/report_generator.py
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@ -1,7 +1,7 @@
from ... import dataclass_utils
from .model_generator import FormData, _DEFAULT_MC_SAMPLE_SIZE
from ... import monte_carlo as mc
from cara import models
from cara import models, monte_carlo
import qrcode
import numpy as np
import matplotlib.pyplot as plt
@ -107,12 +107,14 @@ def img2base64(img_data) -> str:
def plot(times, concentrations, model: models.ExposureModel):
fig = plt.figure()
ax = fig.add_subplot(1, 1, 1)
points = 600
viral_loads = np.linspace(3, 12, points)
viral_loads = np.linspace(2, 12, points)
vl_means = []
vl_medians = []
er_means = []
er_medians = []
lower_percentiles = []
upper_percentiles = []
@ -129,11 +131,10 @@ def plot(times, concentrations, model: models.ExposureModel):
infected=models.InfectedPopulation(
number=1,
presence=models.SpecificInterval(((0, 4), (5, 9))),
mask=False,
mask=models.Mask.types['Type I'],
mask=models.Mask.types['No mask'],
activity=models.Activity.types['Seated'],
virus=models.Virus(
viral_load_in_sputum=vl,
viral_load_in_sputum=10**vl,
infectious_dose=50.,
),
expiration=models.Expiration.types['Breathing']
@ -143,15 +144,23 @@ def plot(times, concentrations, model: models.ExposureModel):
number=2,
presence=models.SpecificInterval(((0, 4), (5, 9))),
activity=models.Activity.types['Seated'],
mask=models.Mask.types['Type I']
mask=models.Mask.types['No mask']
),
)
)
emission_rate = exposure_model.concentration_model.infected.emission_rate_when_present()
vl_means.append(np.mean(emission_rate))
vl_medians.append(np.median(emission_rate))
lower_percentiles.append(np.quantile(emission_rate, 0.01))
upper_percentiles.append(np.quantile(emission_rate, 0.99))
er_means.append(np.mean(emission_rate))
er_medians.append(np.median(emission_rate))
lower_percentiles.append(np.quantile(emission_rate, 0.25))
upper_percentiles.append(np.quantile(emission_rate, 0.75))
ax.plot(viral_loads, er_means)
ax.fill_between(viral_loads, lower_percentiles, upper_percentiles, alpha=0.2)
ax.set_yscale('log')
plt.title('Emission rate vs Viral Load')
plt.ylabel('ER (Virions/h)', fontsize=14)
plt.xticks(ticks=[i for i in range(2, 13)], labels=['$10^{' + str(i) + '}$' for i in range(2, 13)])
plt.xlabel('Viral load (RNA copies mL$^{-1}$)', fontsize=14)
return fig