Measles example

This notebook reproduces a visualization by the Wall Street Journal about the incidence of measles over time, which the brilliant Brian Granger adapted into an example for the Altair library .

Most examples work across multiple plotting backends, this example is also available for:

In [1]:
import numpy as np
import holoviews as hv
import pandas as pd
from holoviews import opts

hv.extension('matplotlib')
hv.output(fig='svg')

Declaring data

In [2]:
url = 'https://raw.githubusercontent.com/blmoore/blogR/master/data/measles_incidence.csv'
data = pd.read_csv(url, skiprows=2, na_values='-')

yearly_data = data.drop('WEEK', axis=1).groupby('YEAR').sum().reset_index()
measles = pd.melt(yearly_data, id_vars=['YEAR'], var_name='State', value_name='Incidence')

heatmap = hv.HeatMap(measles, label='Measles Incidence')
aggregate = hv.Dataset(heatmap).aggregate('YEAR', np.mean, np.std)

vline = hv.VLine(1963)
marker = hv.Text(1964, 800, 'Vaccine introduction', halign='left')

agg = hv.ErrorBars(aggregate) * hv.Curve(aggregate)

Plot

In [3]:
(heatmap + agg * vline * marker).opts(
    opts.HeatMap(aspect=1.4,invert_yaxis=True, show_values=False, show_frame=False,
                 labelled=[], xaxis=None, logz=True),
    opts.Layout(aspect_weight=1, fig_size=300, vspace=0, sublabel_format=None),
    opts.Overlay(aspect=3, show_title=False, bgcolor='white', 
                 show_legend=False, show_frame=False, xrotation=90),
    opts.VLine(color='black', ylim=(0, 1050))).cols(1)
Out[3]:

Download this notebook from GitHub (right-click to download).