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feat(gsea): add pathway genes to GSEA results #29

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Merged
polrus merged 1 commit into from
May 27, 2026
Merged

feat(gsea): add pathway genes to GSEA results #29

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10 changes: 7 additions & 3 deletions app/services/gsea.py
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Original file line number Diff line number Diff line change
Expand Up @@ -244,10 +244,13 @@ def run_gsea_from_dataframe(
else:
res_df["Link"] = "https://www.ebi.ac.uk/chembl/visualise"

# --- Size = number of genes defined in GMT ---
# --- Size and full gene list from GMT ---
res_df["Pathway size"] = res_df["ID"].map(
lambda x: len(id_to_genes.get(x, [])) if pd.notna(x) and x != "" else 0
)
res_df["Pathway genes"] = res_df["ID"].map(
lambda x: ",".join(id_to_genes.get(x, [])) if pd.notna(x) and x != "" else ""
)

rename_map = {
"Term": "Pathway",
Expand All @@ -274,7 +277,8 @@ def run_gsea_from_dataframe(
res_df.groupby(
[
"ID", "Link", "Pathway", "ES", "NES", "FDR", "p-value",
"Sidak's p-value", "Number of input genes", "Leading edge genes", "Pathway size",
"Sidak's p-value", "Number of input genes", "Leading edge genes",
"Pathway size", "Pathway genes",
],
dropna=False,
)["Parent pathway"]
Expand Down Expand Up @@ -310,7 +314,7 @@ def safe_int_col(df_, col_name):
})

# Ensure string columns are properly handled
string_columns = ['Leading edge genes', 'Parent pathway']
string_columns = ['Leading edge genes', 'Pathway genes', 'Parent pathway']
for col in string_columns:
if col in res_df.columns:
res_df[col] = res_df[col].astype(str).replace('nan', '')
Expand Down
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