# fig = px.bar(tests, x='Date', y=['Positives', 'Tests'], barmode='group')
# pplot(fig, include_plotlyjs='cdn', filename=plotpath+'\\temp1.html')
# Make separate lines for each day of the week
# fig = px.line(tests, x='Date', y='Positives', color='Weekday')
# pplot(fig, include_plotlyjs='cdn', filename=plotpath+'\\temp2.html')
#%% Plot tests by result date
# remember below shows 7-day average positivity as average of the positivity,
# not more correctly positivity of the averages.
covid.plotly_twolines(
tests,
'Positivity',
'Positives',
plotcolors=['violet', 'steelblue', 'thistle'],
secondary_scale=3e4,
savefile=plotpath + '\\Pos-Positivity-ByResult-WI.html',
)
# covid.plotly_casetest(sourcedata=tests,
# case_col='Positives',
# test_col='Tests',
# date_col='Date',
# savefile=plotpath + '\\Pos-Test-ByResult-WI.html',
# )
#%% Cases by test date for Wisconsin
filename = 'C:\dev\covid-wisconsin\data\Cases_with_prob_stacked_data_2021-01-08.csv'
wi = pd.read_csv(filename)
marker='.')
#%%
quit()
#%% Plot all cases vs. deaths
savefile = '.\\docs\\assets\\plotly\\Surge-Predictor.html'
fig = covid.plotly_twolines(
state,
'Positivity',
'Cases',
plotcolors=['violet', 'steelblue'],
secondary_scale=1e4,
# plotlabels = {'title': 'Surge Detector<br>(assuming CFR '+str(CFR)+'%)',
# 'yaxis': 'Deaths',
# 'yaxis_secondary': 'Cases',
# },
column1_bar=True,
savefile=savefile,
)
# # save_png = '.\\docs\\assets\\Cases-Deaths-WI_2020-12-06.png'
# save_png = '.\\docs\\assets\\Cases-Deaths-WI.png'
# fig.write_image(
# save_png,
# width=900,
# height=600,
# engine='kaleido',
# )
pos_df = pos_df[pos_df.Date < pos_df.Date.max()]
#%% Plotly plot for cases / positivity
plotpath = '.\\docs\\_includes\\plotly'
savefile = plotpath+'\\Pos-Positivity-WI.html'
fig = covid.plotly_twolines(
pos_df,
'Positive tests',
'Percent positive',
plotcolors=['steelblue', 'darkmagenta', 'lightsteelblue'],
secondary_scale=1/25000,
date_min=datetime.datetime(2021,1,15),
range_max=2000,
col1_mode='avg-bar',
col2_mode='line',
plotlabels = {'title': 'WI Positive Tests and Percent Positive',
'yaxis': 'Positve tests',
'yaxis_secondary': 'Percent positive',
},
savefile=savefile,
showfig=False,
)
fig.update_xaxes(title_text='Date of test result')
fig.update_yaxes(secondary_y=True, tickformat=',.0%')
fig.update_traces(secondary_y=True, hovertemplate='%{y:.1%}')
fig.write_html(
file=savefile,
file=htmlfile,
default_height=500,
default_width=700,
include_plotlyjs='cdn',
)
os.startfile(htmlfile)
fig.write_image(
save_png,
width=700,
height=500,
engine='kaleido',
)
os.startfile(save_png)
#%% Compare cases and hospitalizations?
covid.plotly_twolines(
state,
'POS_NEW',
'HOSP_NEW',
plotcolors=['steelblue', 'darkorange'],
secondary_scale=0.05,
plotlabels=dict(
title='WI Daily Cases and Hospitalizations',
yaxis='Cases',
yaxis_secondary='Hospitalizations',
),
savefile='docs\\assets\\plotly\\Cases-Hosp-WI.html',
)
'POS_NEW': 'Cases',
'TEST_NEW': 'Tests',
'DTH_NEW': 'Deaths',
'HOSP_NEW': 'Hospitalizations'
}
mke = mke.rename(columns=col_rename)
savefile = '.\\docs\\assets\\plotly\\Cases-Hosp-Milwaukee.html'
fig = covid.plotly_twolines(
mke,
'Hospitalizations',
'Cases',
plotcolors=['darkorange', 'steelblue', 'burlywood'],
secondary_scale=10,
plotlabels={
'title': 'Milwaukee Daily Cases and Hospitalizations',
'yaxis': 'Hospitalizations',
'yaxis_secondary': 'Cases',
},
column1_bar=True,
savefile=savefile,
)
fig.add_annotation(
x=datetime.datetime(2020, 5, 11),
y=45,
xanchor='right',
align='right',
text=
'950 hospitalizations<br>from prior days<br>reported on May 11<br>(not pictured)'
)
state = state.set_index('Date')
state[delay_str] = deaths
state = state.reset_index()
#%% Plot all cases vs. deaths
CFR = 1.0
savefile = '.\\docs\\assets\\plotly\\Cases-Deaths-WI.html'
fig = covid.plotly_twolines(
state,
delay_str,
'Cases',
plotcolors=['firebrick', 'steelblue', 'rosybrown'],
secondary_scale=1 / (CFR / 100),
plotlabels={
'title': 'WI Deaths and Cases<br>(assuming CFR ' + str(CFR) + '%)',
'yaxis': 'Deaths',
'yaxis_secondary': 'Cases',
},
column1_bar=True,
savefile=savefile,
)
# save_png = '.\\docs\\assets\\Cases-Deaths-WI_2020-12-06.png'
save_png = '.\\docs\\assets\\Cases-Deaths-WI.png'
fig.write_image(
save_png,
width=900,
height=600,
engine='kaleido',
)
plotpath = '.\\docs\\assets\\plotly'
# covid.plotly_twolines(
# pos_df,
# 'Percent Positive',
# 'Positive',
# plotcolors=['violet', 'steelblue', 'thistle'],
# secondary_scale=300,
# savefile=plotpath+'\\Pos-Positivity-WI.html',
# )
covid.plotly_twolines(
pos_df,
'Positive',
'Percent Positive',
plotcolors=['steelblue', 'violet', 'lightsteelblue'],
secondary_scale=1 / 200,
range_max=8000,
savefile=plotpath + '\\Pos-Positivity-WI.html',
)
covid.plotly_twolines(
pos_df,
'Positive',
'Tests',
plotcolors=['steelblue', 'olivedrab', 'lightsteelblue'],
secondary_scale=10,
range_max=8000,
savefile=plotpath + '\\Pos-Tests-WI.html',
)