Add html compliance report

Snakefile

@@ -37,6 +37,7 @@ rule all:
         expand("reports/figures/{pid}/{sensor}_heatmap_rows.html", pid=config["PIDS"], sensor=config["SENSORS"]),
         expand("reports/figures/{pid}/compliance_heatmap.html", pid=config["PIDS"]),
         expand("reports/figures/{pid}/battery_consumption_rates_barchart.html", pid=config["PIDS"]),
+        expand("reports/compliance/{pid}/compliance_report.html", pid=config["PIDS"]),
 
 rule clean:
     shell:

rules/reports.snakefile

@@ -29,3 +29,12 @@ rule battery_consumption_rates_barchart:
         "reports/figures/{pid}/battery_consumption_rates_barchart.html"
     script:
         "../src/visualization/battery_consumption_rates_barchart.py"
+
+rule compliance_report:
+    input:
+        sensor_heatmaps =  expand("reports/figures/{{pid}}/{sensor}_heatmap_rows.html", sensor=config["SENSORS"]),
+        compliance_heatmap =  rules.compliance_heatmap.output
+    output:
+        "reports/compliance/{pid}/compliance_report.html",
+    script:
+        "../src/visualization/compliance_report.Rmd"

src/visualization/compliance_report.Rmd

@@ -0,0 +1,39 @@
+---
+title: "Compliance Report"
+author:
+    - "MoSHI Pipeline"
+date: "`r format(Sys.time(), '%d %B, %Y')`"
+params:
+   rmd: "compliance_report.Rmd"
+output:
+  html_document:
+  highlight: tango
+  number_sections: no
+  theme: default
+  toc: yes
+  toc_depth: 3
+  toc_float:
+    collapsed: no
+    smooth_scroll: yes
+---
+
+```{r include=FALSE}
+source("packrat/init.R")
+```
+
+## Overall phone compliance
+
+```{r, echo=FALSE}
+htmltools::includeHTML(snakemake@input[["compliance_heatmap"]])
+```
+
+## Per sensor compliance
+```{r, echo=FALSE}
+heatmaps  <- snakemake@input[["sensor_heatmaps"]]
+heatmaps.html <- vector(mode="list", length(heatmaps))
+
+for(sensor_id in 1:length(heatmaps)){
+    heatmaps.html[[sensor_id]] <- htmltools::includeHTML(heatmaps[sensor_id])
+}
+htmltools::tagList(heatmaps.html)
+```