6. Running reporter.py and the seeQc Shiny Application
reporter.py is a simple program which parses the resulting output directory of seQuoia. It is largely just a wrapper for running the forked MultiQC repository tailored to be run with the resulting sample directories of seQuoia's sheppard.py. However, it also produces some simple tab-delimited text files meant for interactive visualization in the Shiny application seeQc.
seeQc is a Shiny application for interactive and flexible visualization of some QC metrics (in the high_level_stats.txt result file) for samples generated by reporter.py.
You can start up the seeQc Shiny App as following:
#!/bin/bash
source /path/to/miniconda3/bin/activate /path/to/seQc_envs/seeQc_Shiny/
## current directory of bash script being called
DIR=$@
export HOSTADDR=`hostname -i`
cmd="Rscript -e 'library(shiny); x <- Sys.getenv(\"HOSTADDR\"); shiny::runApp(appDir=\"$DIR\", host=x, port=5430)'"
cmd2="echo $HOSTADDR"
eval $cmd2
eval $cmd
Centrifuge results can also be accessed via the seeQc application using a heatmap visualization which takes in as input the centrifuge_summary.txt file produced by reporter.py:
