CCC: Decide on an input format

[csangara]

Since many of us prefer working in Python, I propose the input format to be AnnData with the following specifications:

• .X containing raw counts
• .obs containing a column of cell type annotations
• .obsm["spatial'] containing x,y coordinates

[rcannood]

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"]]