log2 fitted mean of one covariate, spots x genes (R normaliseMeanBio/LS/Batch at scale 1).
covariate is "biology", "ls" (library-size effect at the median library size) or "batch". genes is a list of var_names (default all).
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"]),# already fitted with sn.spanorm(adata, sample_p=0.05, df_tps=2)vals = sn.pl.covariate_values(adata, covariate="biology", genes=["MOBP", "ACTB"])vals.shape # spots x genes