dotools_py.get.log2fc

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dotools_py.get.log2fc#

dotools_py.get.log2fc(adata, group_by, reference, groups=None, features=None, layer=None)[source]#

Calculate the log2foldchanges for a set of groups.

Parameters:
adata AnnData

Annotated data matrix.

group_by str

Column in obs to group by.

reference str

Reference condition to use for the calculation.

groups str | list | None (default: None)

Alternative condititons to use. If None, all the condititons will be used.

features str | list | None (default: None)

Features to use for calculating the log2foldchanges. If set to None all features will be used.

layer str | None (default: None)

Layer in the AnnData to use for the calculation.

Return type:

DataFrame

Returns:

Returns a DataFrame with the log2-foldchanges. One column will be added for each condition in groups

Example

>>> import dotools_py as do
>>> adata = do.dt.example_10x_processed()
>>> df = do.get.log2fc(adata, group_by="condition", reference="healthy")
>>> df.head(5)
        genes  log2fc_disease
0  ATP2A1-AS1       26.073313
1      STK17A       -0.429677
2    C19orf18        0.775196
3        TPP2      -22.599501
4       MFSD1       -1.669137
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