Updated README with plot script and protocol.

README.md

@@ -12,7 +12,7 @@ The workflow is managed by Snakemake. Below are brief explanations on the variou
 
 This repository contains configuration files for multiple artifacts from HPC conferences. These configuration files contain multiple informations that are used by ECG to build the Docker container and perform a software environment analysis.
 
-*TODO: talk about the protocol to create one's own config file*
+You can suggest your own configuration files by following the protocol given inside the `protocol` directory (protocol is still WIP).
 
 ### ECG
 
@@ -37,7 +37,7 @@ Multiple type of analysis are done with the output of ECG to create tables that
 
 ### Plots with R
 
-*TODO: write the code...*
+The plotting script can generate both line and bar plots using the analysis results.
 
 ## Setup
 
@@ -150,6 +150,8 @@ Where:
 - `<input_table1>`, `<input_table2>`... are one or more output tables from ECG. The required ECG output depends on the analysis script, see below.
 - `<output_table>` is the path where to store the table generated by the analysis script.
 
+*TODO: explain outputs*
+
 ##### Software environment analysis
 
 The script `softenv_analysis.py` performs a software environment analysis by parsing one or more package lists generated by ECG.
@@ -175,7 +177,16 @@ The table generated by this script gives the amount of images that have been bui
 
 #### Plots with R
 
-*TODO: Write the code...*
+Under the directory `plot`, you will find a `plot.r` script. Run it as follow:
+
+```
+Rscript plot.r <analysis_path> <plot_type> <column1> <column2> ...
+```
+
+Where:
+- `<analysis_path>` is the path to the analysis table produced by an analysis script.
+- `<plot_type>` is either `line` or `bar` depending if you want to produce a line or a bar plot from the given table.
+- `<column1> <column2> ...` are the headers of the columns of the given table.
 
 ## License