recipes

Apply a standard preprocessing recipe to the data.

Parameters

recipe: str Type of preprocessing recipe to apply. Available options are Seurat, Weinrev17 and Zheng17.

log: bool Apply log tranform to data. If data is already logarithmized, set this to False.

n_top_genes: int Number of genes to keep. Used for Zheng17 recipe.

mean_threshold: float mean value for threshold. Used for Weinreb17 recipe.

cv_threshold: float cv value for threshold. Used for Weinreb17 recipe.

n_pcs: int Number of principle components to include. Used for Weinreb17 recipe.

Web view

recipes_screenshot

Python equivalent

import scanpy as sc

# Seurat recipe
sc.pp.recipe_seurat(st.session_state.adata_state.current.adata, log=True) 
# Weinreb17 recipe
sc.pp.recipe_weinreb17(st.session_state.adata_state.current.adata, log=True, mean_threshold=0.01, cv_threshold=2, n_pcs=50)
# Zheng17 recipe
sc.pp.recipe_zheng17(st.session_state.adata_state.current.adata, log=True, n_top_genes=1000)
  