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elsa_4_make_figures.py
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elsa_4_make_figures.py
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from pathlib import Path
import pandas as pd
import matplotlib.pyplot as plt
import seaborn as sns
sns.set_theme()
from utils.elsa_dataset import ELSA_dataset
class Figure_cumulative_hazard(ELSA_dataset):
def __init__(self):
super().__init__()
self.savepath = 'outputs/plots/figure_ELSA_cumulative_incidence/'
def _get_cumulated(self, event):
zero = pd.Series([0])
event = pd.concat([event, zero]).sort_index()
return event.cumsum()
def make_plot(self):
df = self.preprocessed_df
self.N = len(df)
events = df.groupby(['J', 'X']).pid.count()
censored = events.loc[0]
event_1 = events.loc[1]
event_2 = events.loc[2]
event_3 = events.loc[3]
event_123 = event_1 + event_2 + event_3
cumulated_censored = self._get_cumulated(censored)
cumulated_events = self._get_cumulated(event_123)
incidence = cumulated_events/self.N
incidence_1 = self._get_cumulated(event_1)/self.N
incidence_2 = self._get_cumulated(event_2)/self.N
incidence_3 = self._get_cumulated(event_3)/self.N
cumulated_removed = cumulated_censored.add(cumulated_events,
fill_value=0)
survival = self.N - cumulated_removed
fig, ax1 = plt.subplots()
ax2 = ax1.twinx()
ax2.grid(False)
ax1.grid(False)
ax1.bar(survival.index,
survival,
alpha=0.5,
color='tab:gray',
label='Number at risk')
ax2.plot(incidence, label='Cumulative incidence')
ax2.plot(incidence_1, label=self.printed_events[1])
ax2.plot(incidence_2, label=self.printed_events[2])
ax2.plot(incidence_3, label=self.printed_events[3])
ax1.annotate(xy=(survival.index[0]+0.4, survival.iloc[0]),
xycoords='data',
text='Number at risk',
ha="left", va="top",
color='tab:gray')
ax2.annotate(xy=(incidence.index[-1], incidence.iloc[-1]-0.065),
xycoords='data',
text='Cumulative incidence',
ha="right", va="bottom",
color='tab:blue',
rotation=20)
ax2.annotate(xy=(incidence_1.index[-1], incidence_1.iloc[-1]-0.029),
xycoords='data',
text=self.printed_events[1],
ha="right", va="bottom",
color='tab:orange',
rotation=8)
ax2.annotate(xy=(incidence_2.index[-1], incidence_2.iloc[-1]+0.017),
xycoords='data',
text=self.printed_events[2],
ha="right", va="top",
color='tab:green',
rotation=9)
ax2.annotate(xy=(incidence_3.index[-1], incidence_3.iloc[-1]-0.008),
xycoords='data',
text=self.printed_events[3],
ha="right", va="bottom",
color='tab:red',
rotation=6)
ax1.set_ylabel('Number at risk', fontsize=16)
ax2.set_ylabel('Cumulative incidence', fontsize=16)
ax1.set_xlabel('Waves', fontsize=16)
ax1.tick_params(labelsize=16)
ax2.tick_params(labelsize=16)
ax2.set_ylim((0, None))
fig.tight_layout()
Path(self.savepath).mkdir(exist_ok=True, parents=True)
savepath = self.savepath+'/ELSA_cumulative_incidence'
fig.savefig(savepath+'.png')
fig.savefig(savepath+'.pdf')
print(f'Saved {savepath}')
self = Figure_cumulative_hazard()
self.make_plot()