Metabolome Comparison

Comparing Pattern Results to a Provided Metabolome

To view which compounds identified in the patterns were also found in a metabolomics experiment you performed, two inputs are needed:

Inputs

1. A graph_results.csv or the output of python src/run_graph.py in Step 4.

2. CSV containing a list of KEGG compounds that were identified in the metabolome. An example of this file can be found in Data/test_sample/metabolome.csv.

Running the script

To get a list of optional and required arguments run python src/RenderMetabolomeComparison.py -h:

options:
  -h, --help            show this help message and exit
  --patterns PATTERNS   Path to the graph_results.csv
  --metabolome METABOLOME
                        Path to CSV file containing one column of KEGG compounds.
  --output OUTPUT       Path to HTML report file