Hello
I used following line of code to save spatial data into h5 and loaded in python.
in R
dior::write_h5(data, file='scdata.h5', object.type = 'singlecellexperiment')
in Python
adata = diopy.input.read_h5(file = 'scdata.h5')
But it does not show "spatial" data in obsm .
AnnData object with n_obs × n_vars = 100 x 200
obs: 'orig.ident', 'nCount_Spatial', 'nFeature_Spatial', 'cell.ids', 'nCount_SCT', 'nFeature_SCT', 'integrated_snn_res.0.1', 'seurat_clusters', 'integrated_snn_res.0.2', 'integrated_snn_res.0.3', 'integrated_snn_res.0.4', 'integrated_snn_res.0.5', 'integrated_snn_res.0.6', 'integrated_snn_res.0.7', 'integrated_snn_res.0.8', 'integrated_snn_res.0.9', 'ident'
obsm: 'X_pca', 'X_umap'
Hello
I used following line of code to save spatial data into h5 and loaded in python.
in R
dior::write_h5(data, file='scdata.h5', object.type = 'singlecellexperiment')
in Python
adata = diopy.input.read_h5(file = 'scdata.h5')
But it does not show "spatial" data in obsm .
AnnData object with n_obs × n_vars = 100 x 200
obs: 'orig.ident', 'nCount_Spatial', 'nFeature_Spatial', 'cell.ids', 'nCount_SCT', 'nFeature_SCT', 'integrated_snn_res.0.1', 'seurat_clusters', 'integrated_snn_res.0.2', 'integrated_snn_res.0.3', 'integrated_snn_res.0.4', 'integrated_snn_res.0.5', 'integrated_snn_res.0.6', 'integrated_snn_res.0.7', 'integrated_snn_res.0.8', 'integrated_snn_res.0.9', 'ident'
obsm: 'X_pca', 'X_umap'