Add row count heatmap

replace/c1cea3fcfe86b5571beb150353ba28b7289444e5
Meng Li 2019-10-25 11:12:55 -04:00
parent 202b881f34
commit 1952098888
6 changed files with 59 additions and 2 deletions

2
.gitignore vendored
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@ -102,3 +102,5 @@ data/interim/*
!/data/interim/.gitkeep
data/processed/*
!/data/processed/.gitkeep
reports/

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@ -1,6 +1,7 @@
configfile: "config.yaml"
include: "rules/preprocessing.snakefile"
include: "rules/features.snakefile"
include: "rules/reports.snakefile"
rule all:
input:
@ -11,6 +12,7 @@ rule all:
sms_type = config["COM_SMS"]["SMS_TYPES"],
day_segment = config["COM_SMS"]["DAY_SEGMENTS"],
metric = config["COM_SMS"]["METRICS"]),
expand("reports/figures/{pid}/{sensor}_heatmap_rows.html", pid=config["PIDS"], sensor=config["SENSORS"]),
# --- Packrat Rules --- #
## Taken from https://github.com/lachlandeer/snakemake-econ-r

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@ -1,5 +1,5 @@
# Valid database table names
SENSORS: [messages]
SENSORS: [messages, calls]
# Participants to include in the analysis
# You must create a file for each participant

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@ -18,15 +18,23 @@ Jinja2==2.10.3
jinja2-time==0.2.0
jsonschema==3.1.1
MarkupSafe==1.1.1
mkl-fft==1.0.14
mkl-random==1.1.0
mkl-service==2.3.0
more-itertools==7.2.0
numpy==1.17.2
pandas==0.25.2
pbr==5.4.3
plotly==4.2.1
poyo==0.5.0
psutil==5.6.3
pyrsistent==0.15.4
python-dateutil==2.8.0
pytz==2019.3
PyYAML==5.1.2
ratelimiter==1.2.0.post0
requests==2.22.0
retrying==1.3.3
six==1.12.0
smmap2==2.0.5
snakemake==5.7.1

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@ -0,0 +1,10 @@
rule heatmap_rows:
input:
"data/raw/{pid}/{sensor}_with_datetime.csv"
params:
table = "{sensor}",
pid = "{pid}"
output:
"reports/figures/{pid}/{sensor}_heatmap_rows.html"
script:
"../src/visualization/heatmap_rows.py"

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@ -0,0 +1,35 @@
import pandas as pd
import numpy as np
import plotly.io as pio
import plotly.graph_objects as go
def getHourlyRowCount(dates, sensor_data):
hourly_row_count = []
for date in dates:
num_rows = []
daily_rows = sensor_data[sensor_data["local_date"] == date]
for hour in range(24):
hourly_rows = daily_rows[daily_rows["local_hour"] == hour]
num_rows.append(hourly_rows.shape[0])
hourly_row_count.append(num_rows)
return hourly_row_count
def getHourlyRowCountHeatmap(dates, hourly_row_count, sensor_name, pid, output_path):
plot = go.Figure(data=go.Heatmap(z=hourly_row_count,x=[x for x in range(24)],y=dates,colorscale='Viridis'))
plot.update_layout(title="Hourly row count heatmap for " + pid + " for sensor " + sensor_name)
pio.write_html(plot, file=output_path, auto_open=False)
sensor_data = pd.read_csv(snakemake.input[0])
# get current sensor name
sensor_name = snakemake.params["table"]
# get current patient id
pid = snakemake.params["pid"]
# get sorted date list
dates = list(set(sensor_data["local_date"]))
dates.sort()
# get num of rows per hour per day
hourly_row_count = getHourlyRowCount(dates, sensor_data)
# get heatmap
getHourlyRowCountHeatmap(dates, hourly_row_count, sensor_name, pid, snakemake.output[0])