scanpy_plus.tl.gsea module

class scanpy_plus.tl.gsea.Gsea(adata, groupby='leiden', organism='human')

Bases: object

Run GSEA.

Uses Enrichr databases https://gseapy.readthedocs.io/en/latest/introduction.html

Example: gsea = cf.Gsea(adata) gsea.run_gsea() adata = gsea.get_results() gsea.get_results(group=’14’, pcutoff=0.05)

Parameters:

  • adata (AnnData) – The AnnData object containing the data.

  • groupby (str) – The column name in adata.obs to group by. Defaults to ‘leiden’.

  • organism (str) – The organism name. Defaults to ‘mouse’.

  • gene_sets (list) – List of gene sets to use. Defaults to [‘PanglaoDB_Augmented_2021’].

  • de_pval_cutoff (float) – P-value cutoff for differential expression. Defaults to 0.05.

  • de_log2fc_min (float) – Minimum log2 fold change for differential expression. Defaults to 1.

  • top_genes (int) – Number of top genes to consider. Defaults to 100.

  • outdir (str) – Directory to store results. Defaults to None.

  • kwargs – Additional arguments to pass to gseapy.enrichr.

Returns:

inplace. adata.uns[‘gsea’]

Return type:

AnnData

Example

gsea = Gsea(adata) gsea.run_gsea() adata = gsea.get_results() gsea.get_results(group=’14’, pcutoff=0.05)

get_results(adata=None, group=None, pcutoff=0.05)
getdb()

Get available databases

run_gsea(gene_sets=['PanglaoDB_Augmented_2021'], group=None, de_pval_cutoff=0.05, de_log2fc_min=1, top_genes=100, outdir=None, **kwargs)

Run GSEA