besca.get_means¶
- besca.get_means(adata, mycat, condition=None)[source]¶
- Calculates average and fraction expression per category in adata.obs
Based on an AnnData object and an annotation category (e.g. louvain) returns geometric mean expression if .raw values are log as it simply calculates mean of whatever values are stored in .raw. Also returns fraction cells expressing gene per category.
- u parameters
- adata: AnnData
an AnnData object
- mycat: str
the category for stratification (e.g. donor, experiment)
- condition: str
the category to be later compared (e.g. treatment, timepoint)
- average_obs
average gene expression per category
- fraction_obs
fraction cells expressing a gene per category