swnn.quick_preprocess_raw

swnn.quick_preprocess_raw(adata, target_sum=None, hvgs=None, batch_key=None, copy=True, log_first=False, **hvg_kwds)

Go through the data-analysis pipeline, including normalization, HVG selection, and z-scoring (centering and scaling)

Parameters

  • adata (AnnData) – the Anndata object

  • target_sum (Optional[int]) – the target total counts after normalization. If None, after normalization, each observation (cell) has a total count equal to the median of total counts for observations (cells) before normalization.

  • hvgs (Optional[Sequence]) – highly variable genes to be used for dimensionality reduction (centering and PCA)

  • batch_key – a column name in adata.obs specifying the batch labels

  • copy – whether to make a co[y of the input data. if False, the data object will be change inplace.

  • log_first (bool) – for some data distributions, perform log(x+1) before total-count normalization might give a better result (e.g. clustering results may be less affected by the sequencing depths)

  • hvg_kwds – other key-word parameters for sc.pp.highly_variable_genes

Return type

AnnData