Add row count heatmap

.gitignore

@@ -101,4 +101,6 @@ data/raw/*
 data/interim/*
 !/data/interim/.gitkeep
 data/processed/*
-!/data/processed/.gitkeep
+!/data/processed/.gitkeep
+
+reports/

Snakefile

@@ -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

config.yaml

@@ -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

requirements.txt

@@ -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

rules/reports.snakefile

@@ -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"

src/visualization/heatmap_rows.py

@@ -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])