Problems in loading the human heart original dataset into R

[cristalliao]

Dear Professor,

I have encountered some problems in loading the human heart dataset into R. Could you please help me to check what the problem is?

Firstly, I read the original dataset in Python using tutorial code. I treat the "adata_st_list_raw" dataset as the original dataset for each slice 0-8.

And I find this dataset's type is a list, and each element in this list is the AnnData object

So I want to save each element in the list as an h5ad file since I want to read them in R:
For example, I want to save slice0 original dataset as h5ad

I use the code slice_0_raw.write_h5ad('/dski/nobackup/xiaoyinl/STitch3D_analysis_and_dataset/human_dataset_orignal/slice_0_raw.h5ad')
And then in R use the code
Convert("/dski/nobackup/xiaoyinl/STitch3D_analysis_and_dataset/human_dataset_orignal/slice_0_raw.h5ad", dest = "h5seurat", overwrite = F)
But I encountered a very strange error in loading the h5seurat object, it said

"Validating h5Seurat file
Warning: Non-unique features (rownames) present, making uniqueInitializing RNA with data
Adding counts for RNA
Adding scale.data for RNA
Warning: Non-unique features (rownames) present, making uniqueAdding feature-level metadata for RNA
Adding reduction loc_use
Adding cell embeddings for loc_use
Warning: Keys should be one or more alphanumeric characters followed by an underscore, setting key from loc_use_ to locuse_Warning: All keys should be one or more alphanumeric characters followed by an underscore '_', setting key to locuse_Adding miscellaneous information for loc_use
Adding reduction spatial
Adding cell embeddings for spatial
Adding miscellaneous information for spatial
Error in if (!x[[i]]$dims) { : the condition has length > 1"

The main error is "Error in if (!x[[i]]$dims) { : the condition has length > 1"

Do you encounter the same error as me? Do you have any suggestions to solve this problem? Thanks a lot!

[cristalliao]

I think this error means this h5seurat is too big. Or do I have any other solutions to solve this problem? Thanks a lot!

[gefeiwang]

Hi Cristal,

This may be caused by some problem in the LoadH5Seurat function. You can load the data csv files (counts, locations, meta information, etc.) directly into R, or use anndata package to read h5ad files in R to run R packages.

Best,
Gefei

[cristalliao]

Dear Professor Gefei,
Thanks a lot! I will try it in another way. Thanks for your help! Very appreciated!

Best regards,
Cristal