I'd like to use some Python packages in my already processed Seurat data. To this aim, I transformed the Seurat object into AnnData as specified here: https://mojaveazure.github.io/seurat-disk/articles/convert-anndata.html. However, this transformed object has some compatibility problems in Python:
Spatial not detected:
sc.pl.spatial(adata, img_key="hires", color="seurat_clusters", size=1.5)
Genes specified differently and not detected
sc.pl.highest_expr_genes(adata, n_top=20, )
This is my object:
I'm quite new in Python and Python objects and I'm not able to see the problem cause the transformation Seurat-->AnnData seems to be completed. Could you please help me?
Hi all!
I'd like to use some Python packages in my already processed Seurat data. To this aim, I transformed the Seurat object into AnnData as specified here: https://mojaveazure.github.io/seurat-disk/articles/convert-anndata.html. However, this transformed object has some compatibility problems in Python:
Spatial not detected:
sc.pl.spatial(adata, img_key="hires", color="seurat_clusters", size=1.5)Genes specified differently and not detected
sc.pl.highest_expr_genes(adata, n_top=20, )This is my object:
I'm quite new in Python and Python objects and I'm not able to see the problem cause the transformation Seurat-->AnnData seems to be completed. Could you please help me?
Thank you in advance! Best.