Open rcannood opened 2 months ago
Note that you can do many of the same thing R as in Python:
How to read in Python:
import anndata as ad
adata = ad.read_h5ad('path/to/file.h5ad')
# Access celltype
adata.obs['celltype']
# Access spatial coordinates
adata.obsm['spatial']
# Access counts
adata.layers['counts']
How to read in R:
library(anndata)
adata <- read_h5ad('path/to/file.h5ad')
# Access celltype
adata$obs[["celltype"]]
# Access spatial coordinates
adata$obsm[["spatial"]]
# Access counts
adata$layers[["counts"]]
Since many of us prefer working in Python, I propose the input format to be AnnData with the following specifications: