Covid in California
How bad is covid moving around California? What county is the worst?
import pandas as pd
import geopandas
import seaborn as sns
import matplotlib.pyplot as plt
from IPython.display import HTML, display
sns.set()
plt.xkcd()
geo_df = geopandas.read_file("https://raw.githubusercontent.com/plotly/datasets/master/geojson-counties-fips.json")
df = pd.read_csv('https://data.ca.gov/dataset/590188d5-8545-4c93-a9a0-e230f0db7290/resource/926fd08f-cc91-4828-af38-bd45de97f8c3/download/statewide_cases.csv')
df.head()
geo_df.head()
merged_df = pd.merge(df, geo_df, left_on='county', right_on='NAME', how='left')
merged_df.shape
merged_df.head()
from matplotlib.animation import FuncAnimation
plot_data_frames = []
for g, gdf in merged_df[merged_df['STATE'] == '06'].groupby(['date']):
plot_data_frames.append(gdf.sort_values('totalcountconfirmed')[-10:])
counties = sorted(merged_df[merged_df['STATE'] == '06']['county'].unique())
colors = {county: color for county, color in zip(counties, sns.color_palette("tab20", n_colors=len(counties)))}
def get_colors(counties):
return [colors[c] for c in counties]
def nice_axes(ax):
ax.tick_params(labelsize=8, length=0)
ax.set_axisbelow(True)
[spine.set_visible(False) for spine in ax.spines.values()]
def init():
ax.clear()
nice_axes(ax)
# ax.set_ylim(.2, 6.8)
def update(i):
for bar in ax.containers:
bar.remove()
tmp_df = plot_data_frames[i]
ax.barh(
y=[n+0.5 for n in range(10)],
width=tmp_df['totalcountconfirmed'],
tick_label=tmp_df['county'],
color=get_colors(tmp_df['county'].values)
)
date = tmp_df.iloc[0]['date']
ax.set_title(f'COVID-19 Total Cases by County - {date}')
fig = plt.Figure(figsize=(12, 8))
ax = fig.add_subplot()
anim = FuncAnimation(
fig=fig,
func=update,
init_func=init,
frames=len(plot_data_frames),
interval=100,
repeat=False
)
display(HTML(anim.to_jshtml()))
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