glue_genes.glue_single_cell.qt.diff_gene_exp.get_gene_diff_exp#
- glue_genes.glue_single_cell.qt.diff_gene_exp.get_gene_diff_exp(subset1, subset2, data)#
Get differential gene expression for two subsets over a dataset
Uses scanpy rank_genes_groups with just one group (subset1) and one reference set (subset2) and method=wilcoxon.
Note that this copies the relevant subsets into memory as otherwise this won’t work on anndata in disk-backed mode:
(the above is technically for a different scanpy function, but the same problem occurs for rank_genes_groups)
- Parameters:
- subset1
Subset
The highest ranked genes are expressed more in this subset.
- subset2
Subset
The reference subset. The lowest ranked genes are expressed more in this subset.
- data
DataAnnData
The gene expression (X) matrix connecting genes and cells.
- show_warningbool, optional
Whether to show a warning dialog if the subset is not valid. Default is True.
- subset1