dotools_py.pp.sctransform_normalize

dotools_py.pp.sctransform_normalize#

dotools_py.pp.sctransform_normalize(adata, batch_key=None, layer=None)[source]#

Normalization based on SCTransform.

This function performs an alternative normalization based on the SCTransform.

Parameters:
adata AnnData

AnnData object with counts in X.

batch_key str (default: None)

obs metadata with batch information.

layer str (default: None)

layer to use.

Return type:

None

Returns:

Returns None. The input AnnData object will have two new layers containing the SCT counts and normalize data.

Example

>>> import dotools_py as do
>>> adata = do.dt.example_10x_processed()
>>> adata
AnnData object with n_obs × n_vars = 700 × 1851
obs: 'batch', 'condition', 'n_genes_by_counts', 'log1p_n_genes_by_counts', 'total_counts', 'log1p_total_counts',
     'total_counts_mt', 'log1p_total_counts_mt', 'pct_counts_mt', 'total_counts_ribo', 'log1p_total_counts_ribo',
     'pct_counts_ribo', 'n_genes', 'n_counts', 'doublet_class', 'doublet_score', 'leiden', 'cell_type',
     'autoAnnot', 'celltypist_conf_score', 'annotation', 'annotation_recluster'
var: 'mean', 'std', 'highly_variable', 'means', 'dispersions', 'dispersions_norm', 'highly_variable_nbatches',
     'highly_variable_intersection'
uns: 'annotation_colors', 'annotation_recluster_colors', 'batch_colors', 'hvg', 'leiden', 'leiden_colors', 'log1p',
     'neighbors', 'pca', 'umap'
obsm: 'X_CCA', 'X_pca', 'X_umap'
varm: 'PCs'
layers: 'counts', 'logcounts'
obsp: 'connectivities', 'distances'
>>>
>>> do.pp.sctransform_normalize(adata, batch_key="batch", layer="counts")
>>> adata
AnnData object with n_obs × n_vars = 700 × 1181
obs: 'batch', 'condition', 'n_genes_by_counts', 'log1p_n_genes_by_counts', 'total_counts', 'log1p_total_counts',
     'total_counts_mt', 'log1p_total_counts_mt', 'pct_counts_mt', 'total_counts_ribo', 'log1p_total_counts_ribo',
     'pct_counts_ribo', 'n_genes', 'n_counts', 'doublet_class', 'doublet_score', 'leiden', 'cell_type',
     'autoAnnot', 'celltypist_conf_score', 'annotation', 'annotation_recluster'
var: 'mean', 'std', 'highly_variable', 'means', 'dispersions', 'dispersions_norm', 'highly_variable_nbatches',
     'highly_variable_intersection', 'SCT_rm'
obsm: 'SCT_rm'
varm: 'PCs'
layers: 'counts', 'logcounts', 'SCT_norm', 'SCT_counts'
obsp: 'connectivities', 'distances'
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