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generate_plots.py
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generate_plots.py
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import pandas as pd
import matplotlib.pyplot as plt
import os
os.mkdir('output/figures')
measures_df_sex = pd.read_csv('output/measures/measure_pulse_ox_by_sex.csv')
measures_df_region = pd.read_csv(
'output/measures/measure_pulse_ox_by_region.csv')
measures_df_age = pd.read_csv(
'output/measures/measure_pulse_ox_by_age_band.csv')
measures_df_total = pd.read_csv(
'output/measures/measure_pulse_ox_total.csv')
#temporary fix for population not working in Measures
measures_df_total = measures_df_total.groupby(
['date'])['had_pulse_ox', 'population'].sum().reset_index()
measures_df_total['value'] = measures_df_total['had_pulse_ox'] / \
measures_df_total['population']
def to_datetime_sort(df):
df['date'] = pd.to_datetime(df['date'])
df.sort_values(by='date')
to_datetime_sort(measures_df_sex)
to_datetime_sort(measures_df_region)
to_datetime_sort(measures_df_age)
to_datetime_sort(measures_df_total)
def calculate_rate(df, value_col='had_pulse_ox', population_col='population'):
num_per_hundred_thousand = df[value_col]/(df[population_col]/100000)
df['num_per_hundred_thousand'] = num_per_hundred_thousand
calculate_rate(measures_df_sex)
calculate_rate(measures_df_age)
calculate_rate(measures_df_region)
calculate_rate(measures_df_total)
def plot_measures(df, title, filename, column_to_plot, category=False, y_label='Number per 100, 000'):
if category:
for unique_category in df[category].unique():
df_subset = df[df[category] == unique_category]
plt.plot(df_subset['date'], df_subset[column_to_plot])
else:
plt.plot(df['date'], df[column_to_plot])
plt.ylabel(y_label)
plt.xlabel('Date')
plt.xticks(rotation='vertical')
plt.title(title)
if category:
plt.legend(df[category].unique(), bbox_to_anchor=(
1.04, 1), loc="upper left")
else:
pass
plt.savefig(f'output/figures/{filename}.jpeg', bbox_inches='tight')
plt.clf()
plot_measures(measures_df_total, 'Pulse Oximetry use across Whole Population',
'population_rates', 'had_pulse_ox', category=False, y_label='Total Number')
plot_measures(measures_df_sex,
'Pulse Oximetry use by Sex per 100, 000', 'sex_rates', 'num_per_hundred_thousand', category='sex', )
plot_measures(measures_df_region,
'Pulse Oximetry use by Region per 100, 000', 'region_rates', 'num_per_hundred_thousand', category='region')
plot_measures(measures_df_age,
'Pulse Oximetry use by Age Band per 100, 000', 'age_rates', 'num_per_hundred_thousand', category='age_band')