def create_fig_pos_dep(dep_curr, df_code_dep, df_dep_r0, df_pos_fr,
df_dep_sum):
'''Confirmed evolution plots for one departement
data :
- dep_curr : dept.name current (dept that you display)
- df_dep_r0 (date, [ date [Rt by dep.] ])
- df_code_dep (-, [ dept.code, dept.name ])
- pt_fr_test_last (-,
[ p, t, dept.code, dept.name, cases, R0 ]) for last 14 days
- df_pos_fr (date, [ date, [daily cases by dep.] ])
'''
display_msg("create_fig_pos_dep ...")
# choice dept.
dep_num_curr = df_code_dep.loc[df_code_dep["name"] == dep_curr,
"code"].values[0]
# calculation
pos_mean = df_dep_sum[dep_num_curr]
# new input style (temp)
rt_last = df_dep_r0[dep_num_curr][-1]
display_msg("create_fig_rt_dep END.")
return figure_pos(df_pos_fr[dep_num_curr], pos_mean, dep_curr, rt_last)
def create_fig_pos_rate(df_feat_fr, country="France"):
'''
data :
- df_feat_fr (date, [date, pos , test, age_pos] )
pos_rate = 100*df_feat_fr["pos"] / df_feat_fr["test"]
'''
display_msg("create_fig_pos_rate ...")
rate_pos = df_feat_fr["rate_pos"]
fig = make_subplots(specs=[[{"secondary_y": True}]])
fig.add_trace(go.Scatter(x=df_feat_fr["date"],
y=rate_pos.values,
mode='lines',
name="pos. rate",
line=dict(color="red"),
fill='tozeroy'),
secondary_y=False)
fig.add_trace(go.Scatter(x=df_feat_fr["date"],
y=df_feat_fr["age_pos"],
mode='lines',
name='pos. age',
line=dict(color="blue")),
secondary_y=True)
age_last = df_feat_fr[df_feat_fr["age_pos"].notna()]["age_pos"].values[-1]
subtitle_curr = \
f'<i>{df_feat_fr["date"].values[-1]}:</i> ' + \
'pos. rate:<b> {:.1f}</b>'.format(rate_pos.values[-1]) + \
" %<br>mean pos. age:<b> {:.1f}</b>".format(age_last)
fig.update_layout(showlegend=True, font=dict(size=12),
title=dict(text=f"Positive rate and age: <b>{country}</b><br>" + \
subtitle_curr,
xanchor="center", x=0.5, yanchor="top", y=0.95)
)
fig.update_yaxes({
"color": "red",
}, secondary_y=False)
fig.update_yaxes({"color": "blue"}, secondary_y=True)
fig.update_layout(margin={"r": 0, "t": 70, "l": 50})
fig.update_layout(legend_orientation="h", legend=dict(x=0, y=1))
fig.add_annotation(x=0,
y=-0.18,
text="<i>Only global country Curve available<br></i>")
fig.update_annotations(dict(xref="paper", yref="paper", showarrow=False))
display_msg("create_fig_pos_rate END.")
return fig
def update_fr(n_clicks, jsonified_pred, jsonified_pred_all, dropdown_value):
display_msg("UPDATE DATA BUTTON ...")
#logger.info("UPDATE DATA BUTTON ...")
if (dropdown_value != "France"):
raise PreventUpdate
if n_clicks < 1: # no update at loading
display_msg("Nothing to do")
#logger.info("Nothing to do")
display_msg("UPDATE DATA BUTTON END.")
#logger.info("UPDATE DATA BUTTON END.")
return dash.no_update
flag_update = check_update()
# prepare data input
df_feat_fr, str_date_mdl, str_data_date = prepare_data_input(flag_update)
# plot data for positive cases
df_plot, df_plot_pred, df_plot_pred_all, str_date_last = \
prepare_plot_data_pos(df_feat_fr, flag_update)
# prepare plot data for MAPS
df_dep_r0, pt_fr_test_last, dep_fr, df_code_dep, _ = \
prepare_plot_data_map(flag_update)
display_msg("UPDATE DATA BUTTON END.")
#logger.info("UPDATE DATA BUTTON END.")
return str_data_date, \
create_fig_pos(df_plot, df_plot_pred, df_plot_pred_all, str_date_mdl), \
create_fig_map(pt_fr_test_last, dep_fr, str_date_last)
def create_fig_rt_fr(df_feat_fr):
'''Rt evolution plots for france
data :
- df_feat_fr (date, [date, pos] )
'''
display_msg("create_fig_rt_fr ...")
ser_rt = df_feat_fr["Rt"]
sum_last = df_feat_fr["sum_cases"].values[-1]
display_msg("create_fig_rt_fr END.")
return figure_rt(ser_rt, "France", sum_last)
def create_fig_map_kr(df_feat_kr, list_col, label):
'''Graph Rt map France
figure map of confirmed / testers and reproduction number by "départements"
data :
- dep_fr (geo json )
- pt_fr_test_last : pivot table : sum up last 14 days of confirmed cases
'''
display_msg("create_fig_map_kr...")
str_date_last = df_feat_kr.index[-1].strftime("%Y-%m-%d")
# Initialize figure
fig = go.Figure()
# Add Traces
fig.add_trace(
go.Choroplethmapbox(geojson=GEOJSON_KR,
name="positive",
locations=LIST_NAME_GEOJSON,
featureidkey="properties.NAME_1",
z=df_feat_kr.filter(list_col).iloc[-1].values,
marker_opacity=0.7,
marker_line_width=0))
annot_conf=[dict( \
text="South Korea : " + label + f" (up to {str_date_last})",
x=0, xref="paper", y=1, yref="paper",
align="left", showarrow=False,
bgcolor="#FFFFFF")]
fig.update_layout(mapbox_style="carto-positron",
mapbox_zoom=ZOOM_KR,
mapbox_center=LAT_LON_KR)
fig.update_layout(margin={"r": 0, "t": 0, "l": 0, "b": 0})
fig.update_layout(annotations=annot_conf)
fig.update_traces(colorbar=dict(thicknessmode="pixels",
thickness=10,
len=0.8,
x=0.9,
xanchor="left",
xpad=0),
selector=dict(type='choroplethmapbox'))
display_msg("create_fig_map_kr END.")
return fig
def update_tabs(value):
display_msg("update_tabs ...")
#logger.info("update_tabs ...")
if (value == "South Korea"):
'''# load data kr
df_feat_kr = load_df_feat_kr()
# figure mdl
graph_mdl = [""]
# figure map
fig_map = create_fig_map_kr(df_feat_kr, LIST_SUM_GEOJSON,
"<b>Confirmed</b> cases : Sum of last 14 days")
# figure graph
dep_curr = "South Korea"
ser_pos = df_feat_kr["pos"]
ser_sum_pos = df_feat_kr["sum_cases"]
rt_last = df_feat_kr["Rt"].values[-1]
fig_curve = figure_pos(ser_pos, ser_sum_pos, dep_curr, rt_last)
graph_curve = dcc.Graph(id='covid-rt-map-curve',
figure=fig_curve)'''
return get_title(value), "app-hide", "graph-mdl", "app-hide", \
"app-hide", "app-map", "app-graph-map", "app-hide", \
"app-show-block", dcc.Markdown(children=markdown_info_mdl_kr)
else:
'''# prepare input data
df_feat_fr, str_date_mdl, str_data_date = prepare_data_input(False)
# prepare plot data for positive cases
df_plot, df_plot_pred, df_plot_pred_all, str_date_last = \
prepare_plot_data_pos(df_feat_fr, False)
# prepare plot data for MAPS
df_dep_r0, pt_fr_test_last, dep_fr, df_code_dep, df_dep_sum = \
prepare_plot_data_map(False)
df_pos_fr = pd.read_csv(PATH_DF_POS_FR)
df_pos_fr.index = df_pos_fr["date"]'''
return get_title(value), "graph-mdl", "app-hide", "app-map", \
"app-graph-map", "app-hide", "app-hide", "app-show-block", \
"app-hide", dcc.Markdown(children=markdown_info_mdl)
def create_fig_rt_dep(dep_curr, df_code_dep, pt_fr_test_last, df_dep_r0):
'''Rt evolution plots for one departement
data :
- df_dep_r0 (date, date / dep. Rt)
- df_code_dep (-, dep. code / dep name )
- pt_fr_test_last (-, p / t / dep / code / name / p_0 / R0)
'''
display_msg("create_fig_rt_dep ...")
dep_num_curr = df_code_dep.loc[df_code_dep["name"] == dep_curr,
"code"].values[0]
ser_rt = df_dep_r0[dep_num_curr]
sum_pos_last = pt_fr_test_last.loc[ \
pt_fr_test_last.dep == dep_num_curr, "p"].values[0]
display_msg("create_fig_rt_dep END.")
return figure_rt(ser_rt, dep_curr, sum_pos_last)
def display_click_data(clickData, n_clicks, fig, graph_type_old, id_button_old,
mode_country_old, dep_old, hoverData):
display_msg(" ")
display_msg("display_click_data ...")
#logger.info("display_click_data ...")
print("clickData: ", clickData)
print("hoverData: ", hoverData)
# get context :
# if "div-rt-map" => user clicked on buttons
# if "covid-rt-map" => user clicked on data
ctx = dash.callback_context
if not ctx.triggered:
button_id = 'No clicks yet'
else:
button_id = ctx.triggered[0]['prop_id'].split('.')[0]
print("button_id: ", button_id)
# check current dept.:
try:
dep_curr = clickData["points"][0]["location"]
except:
dep_curr = "Paris"
print(dep_curr)
# treat graph type :
(a,) = fig["layout"]["updatemenus"]
id_button = a["active"]
if id_button < 3:
graph_type = id_button
else:
graph_type = graph_type_old
print('id_button (old): ', id_button_old)
print('id_button (new): ', id_button)
print("graph_type (old):", graph_type_old)
print("graph_type (new):", graph_type)
# if click change to France button, display Country not dept.
if (id_button_old !=4) & (id_button==4):
mode_country = 1
if (dep_curr != dep_old):
mode_country = 0
else:
mode_country = 1
# if no change for buttons or graph type but change dept
# then displays dept.
elif (id_button_old == id_button) & (graph_type_old == graph_type):
if (dep_curr != dep_old):
mode_country = 0
else:
mode_country = 1
elif (id_button_old != id_button) & (id_button == 0):
mode_country = 0
else:
mode_country = mode_country_old
print("mode_country: ", mode_country)
# buttons Zoom (IDF or DOM-TOM) (prevent update)
if ((id_button == 3) | (id_button == 5)) & (button_id == "div-rt-map"):
print("PreventUpdate.")
return dash.no_update, dash.no_update, graph_type, id_button, \
mode_country, dep_curr
# si type graph Rt
if (graph_type == 2):
if (mode_country == 1):
# load from disk
df_feat_fr = load_data_pos()
fig_out = create_fig_rt_fr(df_feat_fr)
else:
# prepare plot data for MAPS
df_dep_r0, pt_fr_test_last, dep_fr, df_code_dep, _ = \
prepare_plot_data_map(False)
fig_out = create_fig_rt_dep(dep_curr, df_code_dep,
pt_fr_test_last, df_dep_r0)
elif (graph_type == 1):
if (graph_type_old != 1):
df_feat_fr = load_data_pos()
fig_out = create_fig_pos_rate(df_feat_fr)
else:
print("PreventUpdate.")
return dash.no_update, dash.no_update, graph_type, id_button, \
mode_country, dep_curr
# user in mode Confirmed, only dept. available
else:
# if user in mode "Confirmed"
#
# prepare plot data for MAPS
if not mode_country:
df_dep_r0, pt_fr_test_last, dep_fr, df_code_dep, df_dep_sum = \
prepare_plot_data_map(False)
df_pos_fr = pd.read_csv(PATH_DF_POS_FR)
df_pos_fr.index = df_pos_fr["date"]
fig_out = create_fig_pos_dep(dep_curr, df_code_dep,
df_dep_r0, df_pos_fr, df_dep_sum)
else:
print("PreventUpdate.")
return dash.no_update, dash.no_update, graph_type, id_button, \
mode_country, dep_curr
if dep_curr is None:
dep_curr =""
display_msg("display_click_data END.")
#logger.info("display_click_data END.")
return "", fig_out, graph_type, id_button, mode_country, dep_curr
def update_map_kr_callback(n_clicks, dropdown_value, clickData,
n_clicks_country, n_clicks_test, n_clicks_rt, n_clicks_update, graph_type):
if (dropdown_value != "South Korea"):
raise PreventUpdate
display_msg("update_map_kr_callback_callback...")
#logger.info("update_map_kr_callback_callback...")
# take context button
ctx = dash.callback_context
if not ctx.triggered:
button_id = 'No clicks yet'
else:
button_id = ctx.triggered[0]['prop_id'].split('.')[0]
print("button_id: ", button_id)
str_date_kr = dash.no_update
# if update button : update KR data only
if (button_id == "update-data"):
#update_df_feat_kr()
# prepare input data KR (update if available)
df_feat_kr, str_date_mdl_kr, str_data_date_kr = \
prepare_data_input_kr(flag_update=True)
else:
df_feat_kr = None
# graph-type
if (button_id == "btn-conf"):
graph_type = 0
elif (button_id == "btn-test"):
graph_type = 1
elif (button_id == "btn-rt"):
graph_type = 2
print("graph_type: ", graph_type)
# check current dept.:
try:
if (button_id == "btn-kr"):
dep_curr = "South Korea"
else:
dep_curr = clickData["points"][0]["location"]
dep_curr = DICT_AREA[dep_curr]
except:
dep_curr = "South Korea"
print(dep_curr)
# figure curve confirmed
if (graph_type == 0):
# figure map
if (button_id != "covid-rt-map-kr"):
if (df_feat_kr is None):
df_feat_kr = load_df_feat_kr()
fig_map = create_fig_map_kr(df_feat_kr, LIST_SUM_GEOJSON,
"<b>Confirmed</b> cases : Sum of last 14 days")
else:
fig_map = dash.no_update
if (dep_curr == "South Korea"):
if (df_feat_kr is None):
df_feat_kr = load_df_feat_kr()
ser_pos = df_feat_kr["pos"]
ser_sum_pos = df_feat_kr["sum_cases"]
rt_last = df_feat_kr["Rt"].values[-1]
fig_curve = figure_pos(ser_pos, ser_sum_pos, dep_curr, rt_last)
else:
if (df_feat_kr is None):
df_feat_kr = load_df_feat_kr()
ser_pos = df_feat_kr[dep_curr]
ser_sum_pos = df_feat_kr[f"sum_{dep_curr}"]
rt_last = df_feat_kr[f"Rt_{dep_curr}"].values[-1]
fig_curve = figure_pos(ser_pos, ser_sum_pos, dep_curr, rt_last)
elif(graph_type == 1): # test pos rate
# map
fig_map = dash.no_update
# curve
if (df_feat_kr is None):
df_feat_kr = load_df_feat_kr()
fig_curve = create_fig_pos_rate(df_feat_kr, "South Korea")
elif(graph_type == 2): # mode Rt
# figure map
if (button_id != "covid-rt-map-kr"):
if (df_feat_kr is None):
df_feat_kr = load_df_feat_kr()
fig_map = create_fig_map_kr(df_feat_kr, LIST_RT_GEOJSON,
"<b>Rt</b> estimated for last 14 days")
else:
fig_map = dash.no_update
if (dep_curr == "South Korea"):
if (df_feat_kr is None):
df_feat_kr = load_df_feat_kr()
dep_curr = "South Korea"
ser_rt = df_feat_kr[df_feat_kr["date"] >= "2020-03-19"]["Rt"]
sum_pos_last = df_feat_kr["sum_cases"].values[-1]
fig_curve = figure_rt(ser_rt, dep_curr, sum_pos_last,
country="South Korea")
else:
if (df_feat_kr is None):
df_feat_kr = load_df_feat_kr()
ser_rt = df_feat_kr[df_feat_kr["date"] >= \
"2020-03-19"][f"Rt_{dep_curr}"]
sum_pos_last = df_feat_kr[f"sum_{dep_curr}"].values[-1]
fig_curve = figure_rt(ser_rt, dep_curr, sum_pos_last,
country="South Korea")
if ((button_id == "update-data") & (df_feat_kr is not None)):
str_date_kr = f'(up to: {df_feat_kr["date"].values[-1]})'
# prepare plot data for positive cases KR
df_plot_kr, df_plot_pred_kr, df_plot_pred_all_kr, str_date_last_kr = \
prepare_plot_data_pos_kr(df_feat_kr, flag_update=True)
# update graph pos mdl
fig_mdl = create_fig_pos(df_plot_kr, df_plot_pred_kr,
df_plot_pred_all_kr, str_date_mdl_kr, "South-Korea")
return "", fig_map, fig_curve, graph_type, str_date_kr, fig_mdl
else:
# no need to update graph pos mdl
return "", fig_map, fig_curve, graph_type, str_date_kr, dash.no_update
def startup_layout():
'''
startup web page
'''
display_msg("STARTUP...")
#logger.info("STARTUP...")
try:
# update
if settings.MODE_FORCE_UPDATE:
flag_update = True
flag_update_kr = True
else:
flag_update = check_update()
flag_update_kr = check_update_kr()
# prepare input data
df_feat_fr, str_date_mdl, str_data_date = prepare_data_input(flag_update)
# prepare plot data for positive cases
df_plot, df_plot_pred, df_plot_pred_all, str_date_last = \
prepare_plot_data_pos(df_feat_fr, flag_update)
# prepare plot data for MAPS
df_dep_r0, pt_fr_test_last, dep_fr, df_code_dep, df_dep_sum = \
prepare_plot_data_map(flag_update)
df_pos_fr = pd.read_csv(PATH_DF_POS_FR)
df_pos_fr.index = df_pos_fr["date"]
# prepare input data KR
df_feat_kr, str_date_mdl_kr, str_data_date_kr = \
prepare_data_input_kr(flag_update=flag_update_kr)
# prepare plot data for positive cases KR
df_plot_kr, df_plot_pred_kr, df_plot_pred_all_kr, str_date_last_kr = \
prepare_plot_data_pos_kr(df_feat_kr, flag_update=flag_update_kr)
str_country = "France"
display_msg("STARTUP END.")
#logger.info("STARTUP END.")
except Exception as e:
#logger.error("ERROR STARTUP: " + str(e))
raise(e)
return html.Div(children=[
dcc.Location(id='url', refresh=False),
html.H1(children=get_title(str_country), id="app-title"),
html.Div(children=dcc.Dropdown(
id='country-dropdown',
options=[
{'label': 'France', 'value': 'France'},
{'label': 'South Korea', 'value': 'South Korea',
"disabled": False, "title": "Coming soon..."}
],
value=str_country, clearable=False, searchable=False,
), style={'float': 'left', 'width': 120, 'margin-right': 10}),
html.Div(children=html.Button('Update', id='update-data',
n_clicks=0), style={'display': 'inline-block', 'margin-right': 10}),
html.Div(children=dcc.Loading(
id="loading-fig-pos",
type="default",
children=[html.Div(id="loading-output-1", children=str_data_date),
html.Div(id="loading-output-kr", children=str_data_date_kr,
className="app-hide")]),
style={'display': 'inline-block', 'margin-right': 10}),
html.Div(children=html.A(
children="By Gregory LANG, Data Scientist Freelance",
href="https://greg.coolplace.fr/data-scientist-freelance",
target="_blank"), style={'display': 'inline-block'}),
dcc.Tabs(id='tabs-app', value='tab-mdl', children=[
dcc.Tab(id="tab-mdl",
label='Evolution & Model',
value='tab-mdl',
children=[
dcc.Graph(id='covid-pos-graph',
figure=create_fig_pos(df_plot, df_plot_pred,
df_plot_pred_all, str_date_mdl),
className="graph-mdl"
),
dcc.Graph(id='covid-pos-graph-kr', className="app-hide",
figure=create_fig_pos(df_plot_kr, df_plot_pred_kr,
df_plot_pred_all_kr, str_date_mdl_kr,
area="South-Korea")),
html.Div(id='info_mdl',
children=dcc.Markdown(children=markdown_info_mdl))
]
),
dcc.Tab(id="tab-map",
label='Maps',
value='tab-map', children=[
html.Div(id="div-rt-map",
children=[
dcc.Graph(id='covid-rt-map',
figure=create_fig_map(pt_fr_test_last, dep_fr,
str_date_last),
)],
n_clicks=0,
className="app-map"
),
html.Div(id="div-rt-map-kr",
children=[
html.Button('Confirmed', id='btn-conf', n_clicks=0,
style={"padding-right": 15, "padding-left": 15}),
html.Button('Tested', id='btn-test', n_clicks=0,
style={"padding-right": 15, "padding-left": 15}),
html.Button('Rt', id='btn-rt', n_clicks=0,
style={"padding-right": 15, "padding-left": 15}),
html.Button('South Korea', id='btn-kr', n_clicks=0,
style={"padding-right": 15, "padding-left": 15}),
dcc.Graph(id='covid-rt-map-kr')
],
n_clicks=0,
className="app-hide"
),
html.Div(id="div-rt-curve",
children=[
dcc.Loading(id="loading-graph-map", type="default"),
dcc.Graph(id='covid-rt-dep-graph',
figure=create_fig_pos_dep("Paris", df_code_dep,
df_dep_r0, df_pos_fr, df_dep_sum)
)
],
className="app-graph-map"
),
html.Div(id="div-rt-curve-kr",
children=[
dcc.Loading(id="loading-graph-map-kr", type="default"),
dcc.Graph(id='covid-rt-dep-graph-kr')
],
className="app-hide"
)
])
], style={'margin-top': 10}),
# Hidden div inside the app that stores the intermediate value
html.Div(id='predicted-value', style={'display': 'none'},
children=jsonifed_pred(df_plot_pred)),
html.Div(id='predicted-value-all', style={'display': 'none'},
children=jsonifed_pred(df_plot_pred_all)),
html.Div(id='graph_type', style={'display': 'none'},
children=0),
html.Div(id='graph_type_kr', style={'display': 'none'},
children=0),
html.Div(id='id_button', style={'display': 'none'},
children=0),
html.Div(id='mode_country', style={'display': 'none'},
children=0),
html.Div(id='dep', style={'display': 'none'},
children=""),
html.Div(id='info',
children=dcc.Markdown(children=markdown_info))
])
def create_fig_rt(df_dep_r0, df_code_dep, pt_fr_test_last):
display_msg("create_fig_rt...")
list_num_dep = df_dep_r0.columns[1:].tolist()
# path 975 & 977 & 978 doesn't exist in dep name data
list_num_dep.remove('975')
list_num_dep.remove('977')
list_num_dep.remove('978')
list_name_dep = [f'{dep_num_curr} - ' + \
df_code_dep.loc[df_code_dep["code"] == dep_num_curr,
"name"].values[0] + \
"<br>Rt=<b>{:.2f}</b>".format(df_dep_r0[dep_num_curr][-1]) + \
" cases={}".format(pt_fr_test_last.loc[ \
pt_fr_test_last.dep == dep_num_curr, "p"].values[0]) \
for dep_num_curr in list_num_dep]
nb_dep = len(list_num_dep)
nb_col = 4
nb_row = math.ceil(nb_dep / nb_col)
fig = make_subplots(rows=nb_row,
cols=nb_col,
shared_xaxes=True,
shared_yaxes=True,
subplot_titles=list_name_dep)
I_dep = 0
#list_color = []
for row in range(nb_row):
for col in range(nb_col):
dep_num_curr = list_num_dep[I_dep]
dep_curr = df_code_dep.loc[df_code_dep["code"] == dep_num_curr,
"name"].values[0]
if (df_dep_r0[dep_num_curr][-1] > 1) & \
(pt_fr_test_last.loc[ \
pt_fr_test_last.dep == dep_num_curr, "p"].values[0] > 400):
color_curr = "red"
elif (df_dep_r0[dep_num_curr][-1] > 1):
color_curr = "orange"
else:
color_curr = "blue"
fig.add_trace(go.Scatter(x=df_dep_r0["date"],
y=df_dep_r0[dep_num_curr],
mode='lines',
name=dep_curr,
line=dict(color=color_curr),
fill='tozeroy'),
row=row + 1,
col=col + 1)
fig.add_trace(go.Scatter(
x=[df_dep_r0["date"][0], df_dep_r0["date"][-1]],
y=[1, 1],
mode='lines',
line=dict(color="red", dash='dash'),
hoverinfo="skip"),
row=row + 1,
col=col + 1)
I_dep += 1
if I_dep >= nb_dep: #nb_dep:
break
if I_dep >= nb_dep: #nb_dep:
break
#fig.update_traces(patch=dict(font=dict(size=6)))
for I, subplot_title_curr in enumerate(fig['layout']['annotations']):
subplot_title_curr['font'] = dict(size=10)
subplot_title_curr['xshift'] = 0
subplot_title_curr['yshift'] = -10
fig.update_layout(
height=1800,
title="Rt: Estimated Reproduction Nb. in France ( until {} )".format( \
df_dep_r0['date'].max()),
showlegend=False,
font=dict(
size=12,
)
)
display_msg("create_fig_rt END.")
return fig
def create_fig_pos(df_plot,
df_plot_pred,
df_plot_pred_all,
str_date_mdl,
area="France"):
display_msg("create_fig_pos...")
# Create figure with secondary y-axis
fig = make_subplots(specs=[[{"secondary_y": True}]])
# Create and style traces
# total
fig.add_trace(go.Scatter(x=df_plot["date"].astype(np.datetime64),
y=df_plot["nb_cases"],
mode='lines+markers',
line_shape='linear',
line_color="blue",
connectgaps=True,
name="Total"),
secondary_y=False)
fig.add_trace(go.Scatter(x=df_plot_pred_all["date"].astype(np.datetime64),
y=df_plot_pred_all["nb_cases"],
mode='lines+markers',
line_shape='hv',
line_color="red",
connectgaps=True,
name="Total (estim.)"),
secondary_y=False)
fig.add_trace(go.Scatter(x=df_plot_pred["date"].astype(np.datetime64),
y=df_plot_pred["nb_cases"],
mode='lines+markers',
line_shape='hv',
line_color="orange",
connectgaps=True,
name="Total (future estim.)"),
secondary_y=False)
# new cases
fig.add_trace(go.Bar(x=df_plot["date"].astype(np.datetime64),
y=df_plot["pos"],
name="Daily",
opacity=0.33,
marker_color="blue"),
secondary_y=True)
fig.add_trace(go.Bar(x=df_plot_pred["date"].astype(np.datetime64),
y=df_plot_pred["pos"],
name="Daily (future estim.)",
opacity=0.33,
marker_color="orange"),
secondary_y=True)
fig.add_trace(go.Scatter(x=df_plot_pred_all["date"].astype(np.datetime64),
y=df_plot_pred_all["pos"],
mode='lines+markers',
marker_symbol="cross",
line_color="red",
opacity=0.33,
connectgaps=True,
name="Daily (estim.)"),
secondary_y=True)
# Edit the layout
title_fig = f'<b>COVID-19 Confirmed cases in {area}</b>' + \
'<br>Model trained until <b>' + str_date_mdl + '</b>' + \
'<br>predicts next {} days with last {} days until <b>' \
.format(FUTURE_TARGET, PAST_HISTORY) + \
df_plot_pred["date"].max() + '</b>'
fig.update_layout(title=title_fig, yaxis_title='nb <b>Total</b> cases')
fig.update_layout(legend_orientation="h", legend=dict(x=0, y=1))
fig.update_layout(height=600)
fig.update_yaxes(title_text="nb <b>Daily</b> cases", secondary_y=True)
display_msg("create_fig_pos END")
return fig
def create_fig_map(pt_fr_test_last, dep_fr, str_date_last):
'''Graph Rt map France
figure map of confirmed / testers and reproduction number by "départements"
data :
- dep_fr (geo json )
- pt_fr_test_last : pivot table : sum up last 14 days of confirmed cases
'''
display_msg("create_fig_map...")
lat_lon_fr = {'lat': 47, 'lon': 2}
zoom_fr = 4.25
mapbox_args_fr = {
'center': lat_lon_fr,
'style': 'carto-positron',
'zoom': zoom_fr
}
mapbox_args_idf = {
'center': {
'lat': 48.86,
'lon': 2.33
},
'style': 'carto-positron',
'zoom': 7
}
mapbox_args_dom = {
'center': {
'lat': 17,
'lon': -2
},
'style': 'carto-positron',
'zoom': 2
}
# Initialize figure
fig = go.Figure()
# Add Traces
fig.add_trace(
go.Choroplethmapbox(geojson=dep_fr,
name="positive",
locations=pt_fr_test_last["name"],
featureidkey="properties.nom",
z=pt_fr_test_last["p"],
marker_opacity=0.7,
marker_line_width=0))
fig.add_trace(
go.Choroplethmapbox(geojson=dep_fr,
name="tested",
locations=pt_fr_test_last["name"],
featureidkey="properties.nom",
z=pt_fr_test_last["t"],
marker_opacity=0.7,
marker_line_width=0,
visible=False))
fig.add_trace(
go.Choroplethmapbox(geojson=dep_fr,
name="Rt",
locations=pt_fr_test_last["name"],
featureidkey="properties.nom",
z=pt_fr_test_last["R0"],
zmin=.5,
zmax=1.5,
marker_opacity=0.7,
marker_line_width=0,
visible=False))
annot_conf=[dict( \
text="France : <b>Confirmed</b> cases (Total for 14 days before " + \
f"{str_date_last})",
x=0, xref="paper", y=1, yref="paper",
align="left", showarrow=False,
bgcolor="#FFFFFF")]
annot_test=[dict( \
text="France : <b>Tested</b> cases (Total for 14 days before " + \
f"{str_date_last})", x=0, xref="paper", y=1, yref="paper",
align="left", showarrow=False,
bgcolor="#FFFFFF")]
annot_r0=[dict( \
text="France : <b>Rt</b> estimated for 14 days before " + \
f"{str_date_last})", x=0, xref="paper", y=1, yref="paper",
align="left", showarrow=False,
bgcolor="#FFFFFF")]
fig.update_layout(updatemenus=[
dict(
type="buttons",
direction="right",
xanchor="left",
y=0.95,
x=0,
active=0,
showactive=True,
buttons=list([
dict(label="Confirmed",
method="update",
args=[{
"visible": [True, False, False]
}, {
"annotations": annot_conf
}]),
dict(label="Tested",
method="update",
args=[{
"visible": [False, True, False]
}, {
"annotations": annot_test
}]),
dict(label="Rt",
method="update",
args=[{
"visible": [False, False, True]
}, {
"annotations": annot_r0
}]),
dict(label="Zoom : IdF",
method="relayout",
args=[{
"mapbox": mapbox_args_idf
}]),
dict(label="France",
method="relayout",
args=[{
"mapbox": mapbox_args_fr
}]),
dict(label="DOM-TOM",
method="relayout",
args=[{
"mapbox": mapbox_args_dom
}]),
]),
)
])
fig.update_layout(mapbox_style="carto-positron",
mapbox_zoom=zoom_fr,
mapbox_center=lat_lon_fr)
fig.update_layout(margin={"r": 0, "t": 0, "l": 0, "b": 0})
fig.update_layout(annotations=annot_conf)
fig.update_traces(colorbar=dict(thicknessmode="pixels",
thickness=10,
len=0.8,
x=0.9,
xanchor="left",
xpad=0),
selector=dict(type='choroplethmapbox'))
display_msg("create_fig_map END.")
return fig
