Agile Metabolic Health Blood Pressure Dashboard Demo¶
Note: this cell has custom styling that makes it not show up in the Voilà Dashboard. You can hide any other markdown in this notebook by surrounding it with the same “demo-info” class ID as this one.
This dashboard fetches and displays blood pressure data for a patient.
(DEMO) To edit the dashboard:
click here to open the notebook
edit the notebook
save changes
reload this page
To add goals to the demo, add include_goal=True to the last cell in this notebook to select a patient, edit the cell below that sets patient_id , study_id. You can see values in the JupyterHealth Exchange Portal.
import os
import ipywidgets as W
from IPython.display import HTML, Image, Markdown, display
# Convenience function to display markdown
def md(s):
display(Markdown(s))
# Use "if not VOILA:" blocks to print debug/private output
# Otherwise all output is by default shown by VOILA
VOILA = os.environ.get("VOILA_REQUEST_URL")from jupyterhealth_client import Code, JupyterHealthClient
client = JupyterHealthClient()
BLOOD_PRESSURE = Code.BLOOD_PRESSURE.value
user_info = client.get_user()from functools import lru_cache
from requests import HTTPError
_width = "500px"
@lru_cache
def _cache_fetch_data(study_id, patient_id):
"""Cache fetching the same data"""
return client.list_observations_df(
patient_id=patient_id, study_id=study_id, code=Code.BLOOD_PRESSURE
)
study_widget = W.Dropdown(
options=[],
layout=W.Layout(width=_width),
description="Study",
)
def _update_study_list(change=None):
value = study_widget.value
options = {}
for study in client.list_studies():
label = f"[{study['id']}] {study['name']}"
options[label] = study["id"]
if not options:
options["<no available studies>"] = None
study_widget.options = options
if value not in options.values():
study_widget.value = next(iter(options.values()))
_update_study_list()
patient_widget = W.Dropdown(
options=[],
description="Patient",
layout=W.Layout(width=_width),
)
def _update_patient_list(change=None):
value = patient_widget.value
options = {}
for patient in client.list_patients():
label = f"{patient['nameFamily']}, {patient['nameGiven']}: {patient['telecomEmail']}"
options[label] = patient["id"]
if not options:
options["<no available patients>"] = None
patient_widget.options = options
if value not in options.values():
patient_widget.value = next(iter(options.values()))
_update_patient_list()
# uncomment to add 'demo-info' class, which hides these from the rendered dashboard
# study_widget.add_class("demo-info")
# patient_widget.add_class("demo-info")
patient_df = None
def _load_data(change=None):
global patient_df
if not study_widget.value or not patient_widget.value:
patient_df = None
return
try:
patient_df = _cache_fetch_data(study_widget.value, patient_widget.value)
except (ValueError, HTTPError):
patient_df = None
if patient_df is not None and len(patient_df) == 0:
patient_df = None
patient_widget.observe(_load_data, names="value")
_load_data()
try:
study_widget.value = 30013 # Jupyter Study
patient_widget.value = 40039 # test user
except Exception:
print(
"Failed to set default study/patient. May not have access. Are you a member of the BIDS organization?"
)
refresh_button = W.Button(
description="Refresh patients and studies", layout=W.Layout(width=_width)
)
def _reload(btn=None):
_update_study_list()
_update_patient_list()
refresh_button.on_click(_reload)
display(study_widget)
display(patient_widget)
display(refresh_button)if not VOILA:
if patient_df is None or not len(patient_df):
raise ValueError("Found no observations!")
display(patient_df.head())# now start the plotting
from datetime import timedelta
from enum import Enum
from functools import partial
from itertools import chain
import altair as alt
import pandas as pd
pd.options.mode.chained_assignment = None
class Goal(Enum):
"""Enum for met/unmet
These strings will be used for the legend.
"""
met = "under"
unmet = "over"
class Category(Enum):
normal = "normal"
elevated = "elevated"
hypertension = "hypertension"
def classify_bp(row):
"""Classify blood pressure"""
# https://www.heart.org/en/health-topics/high-blood-pressure/understanding-blood-pressure-readings
# note from : We can decide to have just normal, elevated and hypertension to begin with
if (
row.diastolic_blood_pressure_value < 80
and row.systolic_blood_pressure_value < 120
):
return Category.normal.value
elif (
row.diastolic_blood_pressure_value < 80
and 120 <= row.systolic_blood_pressure_value < 130
):
return Category.elevated.value
else:
return Category.hypertension.value
def bp_goal(patient_df, goal="140/90"):
"""True/False for blood pressure met goal"""
sys_goal, dia_goal = (int(s) for s in goal.split("/"))
if (patient_df.systolic_blood_pressure_value <= sys_goal) & (
patient_df.diastolic_blood_pressure_value <= dia_goal
):
return Goal.met.value
else:
return Goal.unmet.value
red_yellow_blue = [
"#4a74b4",
"#faf8c1",
"#d4322c",
]
red_blue = [red_yellow_blue[0], red_yellow_blue[-1]]
def bp_over_time(bp, color_scale="category"):
"""Plot blood pressure over time"""
# https://vega.github.io/vega/docs/schemes/#redyellowblue
if color_scale == "category":
domain = [
Category.normal.value,
Category.elevated.value,
Category.hypertension.value,
]
color = alt.Color(
"category:O",
scale=alt.Scale(
domain=domain,
range=red_yellow_blue,
),
)
shape = alt.Shape(
"category:O",
scale=alt.Scale(
domain=domain,
),
)
elif color_scale == "goal":
domain = [Goal.met.value, Goal.unmet.value]
color = alt.Color(
"goal:O",
scale=alt.Scale(domain=domain, range=red_blue),
)
shape = alt.Shape(
"goal:O",
scale=alt.Scale(domain=domain),
)
# heuristic for x-ticks
end_time = bp.effective_time_frame_date_time.max()
end_date = end_time.date()
start_date = bp.effective_time_frame_date_time.min().date()
time_frame_days = (end_date - start_date).total_seconds() / (3600 * 24)
axis_args = {"format": "%Y-%m-%d"}
if time_frame_days < 7:
# minimum of one week
start_date = end_date - timedelta(days=7)
if time_frame_days < 14:
# at least a week
axis_args["tickCount"] = dict(interval="day", step=1)
if 14 <= time_frame_days < 30:
# expand less than a month to 1 month
start_date = end_date - timedelta(days=30)
if time_frame_days > 90:
# at least a few months, label with year-month
axis_args["format"] = "%Y-%m"
x = alt.X(
"effective_time_frame_date_time_local",
title="date",
axis=alt.Axis(
labelAngle=30,
**axis_args,
),
scale=alt.Scale(
domain=[
pd.to_datetime(start_date),
pd.to_datetime(end_date + timedelta(days=1)),
]
),
)
charts = [
[
alt.Chart(bp, title="blood pressure")
.mark_line(color="#333")
.encode(
x=x,
y=alt.Y(f"{which}_blood_pressure_value", title="mmHg"),
),
alt.Chart(bp, title="blood pressure")
.mark_point(filled=True)
.encode(
x=x,
y=alt.Y(f"{which}_blood_pressure_value", title="mmHg"),
color=color,
shape=shape,
tooltip=[
alt.Tooltip("effective_time_frame_date_time_local", title="date"),
alt.Tooltip("systolic_blood_pressure_value", title="Systolic"),
alt.Tooltip("diastolic_blood_pressure_value", title="Diastolic"),
alt.Tooltip("category"),
],
),
]
for which in ("systolic", "diastolic")
]
return alt.layer(*chain(*charts))
def bp_by_tod(bp):
"""Plot blood pressure by time of day"""
tod_tooltip = [
alt.Tooltip(
"mean(diastolic_blood_pressure_value):Q",
title="avg diastolic",
format=".0f",
),
alt.Tooltip(
"mean(systolic_blood_pressure_value):Q", title="avg systolic", format=".0f"
),
alt.Tooltip("count(diastolic_blood_pressure_value)", title="measurements"),
alt.Tooltip("hours(effective_time_frame_date_time_local)", title="hour"),
]
charts = [
alt.Chart(bp, title="by time of day")
.mark_line(point=True)
.encode(
x=alt.X(
"hours(effective_time_frame_date_time_local)",
title="time of day",
scale=alt.Scale(domain=[0, 24]),
),
y=alt.Y(
f"mean({which}_blood_pressure_value):Q",
title=which,
axis=alt.Axis(title=""),
),
tooltip=tod_tooltip,
)
for which in ("systolic", "diastolic")
]
return alt.layer(*charts)
def plot_patient_blood_pressure(patient_df, goal="140/90", color_scale="category"):
"""plot blood pressure, given a patient data frame, as returned by get_patient_data"""
bp = patient_df.loc[patient_df.resource_type == BLOOD_PRESSURE]
bp["category"] = bp.apply(classify_bp, axis=1)
bp["goal"] = bp.apply(partial(bp_goal, goal=goal), axis=1)
return (
(bp_over_time(bp, color_scale=color_scale) | bp_by_tod(bp))
.resolve_scale(y="shared", color="independent", shape="independent")
.configure_point(size=100)
.interactive()
)
if not VOILA:
# show last 30 days of data
end_date = patient_df.effective_time_frame_date_time.max()
display(
plot_patient_blood_pressure(
patient_df[patient_df.effective_time_frame_date_time >= (end_date - timedelta(days=30))],
color_scale="goal",
)
)import ipywidgets as W
def bp_category_style(row):
"""highlight rows by bp category"""
category = Category(row.category)
if category == Category.hypertension:
color = "#fdd"
elif category == Category.elevated:
color = "#ffc"
else:
color = None
return [f"background-color:{color}" if color else None] * len(row)
def bp_goal_style(row):
"""highlight rows by bp category"""
goal = Goal(row.goal)
if goal == Goal.unmet:
color = "#fdd"
else:
color = None
return [f"background-color:{color}" if color else None] * len(row)
def bp_goal_fraction(patient_df, goal="140/90"):
bp = patient_df.loc[patient_df.resource_type == BLOOD_PRESSURE]
sys_goal, dia_goal = (int(s) for s in goal.split("/"))
met_goal = (bp.systolic_blood_pressure_value <= sys_goal) & (
bp.diastolic_blood_pressure_value <= dia_goal
)
return met_goal.sum() / len(bp)
def bp_table_info(patient_df, goal="140/90", color_scale="category"):
"""Display tabular info"""
bp = patient_df.loc[
patient_df.resource_type == BLOOD_PRESSURE,
[
"effective_time_frame_date_time_local",
"systolic_blood_pressure_value",
"diastolic_blood_pressure_value",
],
]
bp["category"] = bp.apply(classify_bp, axis=1)
bp["goal"] = bp["goal"] = bp.apply(partial(bp_goal, goal=goal), axis=1)
# relabel columns
bp.columns = ["date", "systolic", "diastolic", "category", "goal"]
bp["time"] = bp.date.dt.time
bp["date"] = bp.date.dt.date
bp = bp.astype({"systolic": int, "diastolic": int})
label_style = {"font_weight": "bold", "font_size": "150%"}
table = W.Output()
with table:
styled = (
bp.style.hide()
.hide(["category", "goal"], axis="columns")
.format({"time": "{:%H:%M}"})
)
if color_scale == "goal":
styled = styled.apply(bp_goal_style, axis=1)
else:
styled = styled.apply(bp_category_style, axis=1)
display(HTML(styled.to_html(index=False)))
summary = W.Output()
min_idx = bp.systolic.idxmin()
max_idx = bp.systolic.idxmax()
summary_table = pd.DataFrame(
{
"systolic": [
bp.systolic.min(),
bp.systolic.max(),
bp.systolic.mean(),
],
"diastolic": [
bp.diastolic.min(),
bp.diastolic.max(),
bp.diastolic.mean(),
],
"date": [
bp.loc[min_idx].date,
bp.loc[max_idx].date,
"-",
],
}
)
summary_table = summary_table.astype({"systolic": int, "diastolic": int})
summary_table.index = pd.Index(["min", "max", "avg"])
with summary:
display(HTML(summary_table.to_html()))
# calculate goal fraction
at_goal_fraction = bp_goal_fraction(patient_df, goal)
overview = W.Output()
with overview:
display(
HTML(f"<div style='font-size: 250%'>at goal: {at_goal_fraction:.0%}</div>")
)
box_layout = {
"border_left": "1px solid #aaa",
"padding": "8px",
"margin": "8px",
}
right_box = [
W.Label(value="summary", style=label_style),
summary,
]
if color_scale == "goal":
right_box.extend(
[
W.Label(value="overview", style=label_style),
overview,
]
)
layout = W.HBox(
[
W.VBox(
[W.Label(value="Measurements", style=label_style), table],
layout=box_layout,
),
W.VBox(
right_box,
layout=box_layout,
),
]
)
layout.layout.justify_content = "flex-start"
return layout
if not VOILA:
# preview while run interactively (not voila)
display(bp_table_info(patient_df[-100:], color_scale="goal"))import time
def plot_patient(
view=30,
comorbidity=False,
color="goal",
):
if comorbidity:
goal = "130/80"
else:
goal = "140/90"
df = patient_df
if df is None:
patient_id = patient_widget.value
study_id = study_widget.value
if not patient_id:
md("## No patient selected!")
return
if not study_id:
md("## No study selected!")
return
consents = client.get_patient_consents(patient_id)
md_lines = [f"## No data for patient {patient_id} in study {study_id}!", ""]
md_lines.append("Study consents:")
for study in consents["studies"]:
md_lines.append(f" - [{study['id']}] {study['name']}")
if not consents["studies"]:
md_lines.append("- (none)")
md_lines.append("")
md_lines.append("Studies pending consent:")
md_lines.append("")
for study in consents["studiesPendingConsent"]:
md_lines.append(f" - [{study['id']}] {study['name']}")
if not consents["studiesPendingConsent"]:
md_lines.append("- (none)")
md_lines.append("")
md("\n".join(md_lines))
return
last_day = df.effective_time_frame_date_time.dt.date.max()
start_date = last_day - timedelta(days=view)
df = df[df.effective_time_frame_date_time.dt.date >= start_date]
# for demo: scale if current user is too healthy
df = df.copy()
df["systolic_blood_pressure_value"] = (df["systolic_blood_pressure_value"]).astype(
int
)
df["diastolic_blood_pressure_value"] = (
df["diastolic_blood_pressure_value"]
).astype(int)
display(plot_patient_blood_pressure(df, goal=goal, color_scale=color))
display(bp_table_info(df, goal=goal, color_scale=color))
# utterly bizarre: voilá hangs if this returns too quickly
time.sleep(0.5)
if not VOILA:
plot_patient()Everything above here is setup of the demo itself, not part of the demo; this would all be hidden and managed by EHR inputs.
Below here is the actual demo that is meant to show up as a dashboard and meant for display.
# create the interactive chart
def create_dashboard(include_goal=False):
"""
Create the dashboard
only one input: include_goal
if True, include UCSF goal inputs ('after' view)
if False, only include American Heart Association category view
"""
interact_args = {}
if include_goal:
comorbidity_widget = W.Checkbox(
description="Any comorbidities: ASCVD > 10%, Diabetes Mellitus, CKD (EGFR 20-59), Heart Failure"
)
comorbidity_widget.layout.width = "100%"
comorbidity_widget.add_class("added-widget")
color_widget = W.Dropdown(
value="goal", options={"UCSF Goal": "goal", "AHA Category": "category"}
)
color_widget.add_class("added-widget")
interact_args["comorbidity"] = comorbidity_widget
interact_args["color"] = color_widget
else:
interact_args["comorbidity"] = W.fixed(False)
interact_args["color"] = W.fixed("category")
dashboard = W.interactive(
plot_patient,
view={
"Week": 7,
"Month": 30,
"Year": 365,
},
**interact_args,
)
# give it some border to set it off from the demo setup
dashboard.layout.border = "4px solid #cff"
dashboard.layout.padding = "16px 30px"
# rerender on change of widgets outside the interact
patient_widget.observe(lambda change: dashboard.update(), names="value")
study_widget.observe(lambda change: dashboard.update(), names="value")
return dashboardAgile Metabolic JupyterHealth Dashboard¶
md("#### Logged in as practitioner:")
md(f"{user_info['firstName']} {user_info['lastName']} ({user_info['email']})")
md("---")# DEMO: uncomment include_goal=True to add UCSF goals to visualization,
create_dashboard(
include_goal=True,
)# weird: displaying this in a Markdown cell
# causes voila to hang (?!)
display(Image(url="https://jupyterhealth.org/images/PoweredByJupyter.png"))