fast_size_factors

fast_size_factors(adata, layer=None)

Library-size factors (R fastSizeFactors), written to obs["spanorm_size_factors"].

Examples

Note

The code below runs when the site is built, on a small pre-fitted subset of HumanDLPFC (301 genes x 4015 spots; spanorm(sample_p=0.05, df_tps=2), spanorm_svg() and spanorm_pca() already applied) that is fitted once per build and loaded as adata. The outputs are those of the code shown.

import spanormpy as sn
# adata: the HumanDLPFC AnnData (raw counts in X, coordinates in obsm["spatial"])
sn.fast_size_factors(adata)
adata.obs["spanorm_size_factors"].describe()

count    4015.000000
mean        1.000000
std         0.467105
min         0.028311
25%         0.703057
50%         0.993245
75%         1.284613
max         3.039896
Name: spanorm_size_factors, dtype: float64