The pyMEAN package is designed to facilitate semi-automated enrichment analysis for metabolomic experiments.
pyMEAN requires Python 3+ and is unfortunately not compatible with Python 2. If you are still using Python 2, a clever workaround is to install Python 3 and use that instead.
The easiest way of installing pyMEAN is using pip:
pip install pymean
Alternatively, you can use git and pip in unison to get the development branch:
pip install https://github.com/KeironO/pyMEAN
Here's a starting template to get you started:
# Import pyMEAN module into Python.
from pymean import EnrichmentAnalysis
# A compound list of inchikeys.
compound_list = [
"WDJHALXBUFZDSR-UHFFFAOYSA-N", # acetoacetic acid
"UCMIRNVEIXFBKS-UHFFFAOYSA-N", # beta-alanine
"CVSVTCORWBXHQV-UHFFFAOYSA-N", # creatine
"FFDGPVCHZBVARC-UHFFFAOYSA-N", # dimethylglycine
"VZCYOOQTPOCHFL-OWOJBTEDSA-N", # fumaric acid
"DHMQDGOQFOQNFH-UHFFFAOYSA-N", # glycine
"FFFHZYDWPBMWHY-UHFFFAOYSA-N", # l-homocysteine
"XUJNEKJLAYXESH-REOHCLBHSA-N", # l-cysteine
"COLNVLDHVKWLRT-QMMMGPOBSA-N", # l-phenylalanine
"BTNMPGBKDVTSJY-UHFFFAOYSA-N" # phenylpyruvic acid
]
# Create an EnrichmentAnalysis object for the analysis of hsa
ea = EnrichmentAnalysis(compound_list, organism="hsa")
# Run the analysis
ea.run_analysis(pvalue_cutoff=0.05)
# Obtain results (in the format of a pandas dataframe)
resuklts = ea.resultsIf you'd like to plot out your results, take inspiration from the following method:
def plot_enrichment_analysis_results(results: pd.DataFrame, adj_method:str):
fold_enrichment = np.abs(np.log(results["%s adj. p-value" % (adj_method)]))
plt.figure()
plt.title("Metabolite Sets Enrichment Overview")
plt.barh(results["Pathway Name"], fold_enrichment, height=0.5)
plt.xlabel("Fold Enrichment")
plt.yticks(fontsize=6)
plt.tight_layout()
plt.show()
plot_enrichment_analysis_results(results, "fdr_bh")Which will return the following chart:
Code released under the GPLv3.
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