Error when converting spatial data

[lazappi]

I leave here a snippet of code I have written to do so:

# Prepare the custom conversion
## Obs - Metadata
obs_mapping <- colnames(spatial_obj@meta.data)
names(obs_mapping) <- colnames(spatial_obj@meta.data)
print(length(obs_mapping))
print(paste0("Nrow metadata:", nrow(spatial_obj@meta.data)))

## var mapping - Seurat does not often compute var statistics like in sc.pp

## uns mapping - image identidities
### Image data
images = list(lowres=spatial_obj@images$tissue_lowres_image.png@image)

### Scale factors
scalefactors_seurat <- spatial_obj@images$tissue_lowres_image.png@scale.factors
scalefactors = list(fiducial_diameter_fullres=scalefactors_seurat$fiducial, spot_diameter_fullres=scalefactors_seurat$spot,
                    tissue_hires_scalef=scalefactors_seurat$hires, tissue_lowres_scalef=scalefactors_seurat$lowres)
### Metadata
metadata = list(chemistry_description = chemistry_description, software_version = software_version)
spatial_list <- list(list(images=images,metadata=metadata, scalefactors=scalefactors))
names(spatial_list) <- sample_name

spatial_obj@misc[["spatial"]] <-spatial_list

# Obsm mapping - Coordinates
obsm_spatial <- as.matrix(spatial_obj@images$tissue_lowres_image.png@boundaries$centroids@coords[,c("y","x")])
colnames(obsm_spatial) <- NULL
rownames(obsm_spatial) <- colnames(spatial_obj)
print(paste0("Obsm dim:", dim(obsm_spatial)))
## Add it to dim reduction
spatial_obj[["spatial_adata"]] <- CreateDimReducObject(embeddings = obsm_spatial, assay="Spatial",key="spatialadata_")


print(paste0("Count dim",dim(spatial_obj@assays$Spatial$counts)))
print(names(spatial_obj@assays$Spatial@layers))
print(paste0("Objet dim:",dim(spatial_obj)))
# Trying to use custom annotation
adata <- as_AnnData(
  spatial_obj,
  assay_name = "Spatial",#spatial assay
  x_mapping = "counts",
  layers_mapping = c(counts="counts"),
  obs_mapping = obs_mapping,
  var_mapping = TRUE,
  obsm_mapping = list(X_pca = "pca", X_umap = "umap", spatial = "spatial_adata"),
  obsp_mapping = TRUE,
  uns_mapping = c("spatial")
)
print(paste0("Anndata dim ", dim(adata$X)))

However, I had an error when writing this object. But weirdly, the object was still written and seems functional in python environment as I was able to access .X and plot features & metadata.

> write_h5ad(adata,paste0(save_path, sample_name,".h5ad"), mode="a")
Error:
! Unexpected shape for X
ℹ Expected [36601], got [642, 36601]

> rlang::last_trace(drop = FALSE)
<error/rlang_error>
Error:
! Unexpected shape for X
ℹ Expected [36601], got [642, 36601]
---
Backtrace:
    ▆
 1. ├─anndataR::write_h5ad(...)
 2. │ └─object$as_HDF5AnnData(path, compression = compression, mode = mode)
 3. │   └─anndataR:::as_HDF5AnnData(...)
 4. │     └─HDF5AnnData$new(...)
 5. │       └─anndataR (local) initialize(...)
 6. └─anndataR (local) `<fn>`(base::quote(`<dgRMatrx[,36601]>`))
 7.   └─private$.validate_aligned_array(...)
 8.     └─cli::cli_abort(...)
 9.       └─rlang::abort(...)

Have you already experimented such issue? Do you see any way I could change my code?

Thanks a lot!
Best,
Lucie

[lazappi]

The error message suggests some dimensions are not matching up. I would need to go through your code more closely to work out why that might be, fairly likely it is a false positive or some problem on our side. Do you have an example object you could share? A small toy example that reproduces the error would be best but if you can share the object you started with that would also be great.