IGV Snapshot Report

This directory contains report templates to use with the IGV Snapshot output. By default, the reports will look for .png files in the directory ../IGV_Snapshots/, and include each file found in a report output.

If your IGV snapshot directory has a different name or path, you can either adjust the path inside the report template, or make a symlink with that name at that location.

PDF Output

A PDF report can be generated using the included report.Rnw. Compile it with the command:

./compile_Rnw_report.sh

This report requires LaTeX to be installed with the standalone package. If you are using Linux, or a Linux-style system, and you already have LaTeX installed, you can install this package with the included Makefile with the command:

make install

HTML Output

An HTML formatted report can be generated with the included report.Rmd file. Compile it with the included script:

# module load pandoc/1.13.1
./compile_Rmd_report.R

Software

Software used in report creation

• R programming langauge

  • Hmisc, knitr packages

• LaTeX

  • standalone package

• pandoc 1.13.1+