Open songnsnow opened 2 weeks ago
Could you please check the shape of adata_ev and adata_cell that you input for SEVtras.ESAI_calculator by following code?
print(adata_ev)
print(adata_cell)
There may be a mismatch problem between the two adata objects.
Here is the output from print(adata_ev)
and print(adata_cell)
.
>>> print(adata_ev)
AnnData object with n_obs × n_vars = 4383 × 24040
obs: 'n_genes_by_counts', 'total_counts', 'total_counts_mt', 'pct_counts_mt', 'total_counts_ribo', 'pct_counts_ribo', 'n_genes', 'score', 'batch', 'sEV', 'score1'
>>> print(adata_cell)
AnnData object with n_obs × n_vars = 36076 × 31706
obs: 'orig.ident', 'nCount_RNA', 'nFeature_RNA', 'raw_batch_number', 'n_genes_by_counts', 'total_counts', 'total_counts_mt', 'pct_counts_mt', 'total_counts_ribo', 'pct_counts_ribo', 'n_genes', 'score', 'batch', 'sEV', 'score1', 'barcode_prefix', 'batch_number', 'cell.barcode', 'sample.id', 'sample.id.new', 'Paper_ID', 'Sample', 'percent.mito', 'percent.ribo', 'G1.S.score_Whitfield', 'G2.M.score_Whitfield', 'S.Score', 'G2M.Score', 'Phase', 'Paper_group', 'Paper_subgroup', 'Location', 'Age_group', 'Sex', 'Technology', 'Consensus_Jessa', 'Consensus_Pombo_Raw', 'CAWPE_Score_Pombo', 'Class', 'Celltype', 'celltype', 'Level2_Celltype', 'clst_itg', 'seurat_clusters', 'UMAP_1', 'UMAP_2'
obsm: 'X_pca', 'X_umap'
At the moment I can't figure out what the bug is. Would it be convenient to share testing adata objects for me? I'll test it in my environment. The address is ruiqiaohe#gmail.com (change # to @).
Hi, I've been trying to run the second part (SEVtras.ESAI_calculator) of the tool, but I am getting the error below.
I looked into the deconvolver function, and I believe the error is caused by empty tmp_times Series. I think some of the rows (cells) in near_neighbor_dat are not tracing back to a celltype value, which might be causing the error.
Also, I noticed that the X_pca and X_umap values of adata_cell is not being utilized at least up until the deconvolver function, since adata_combined is being reprocessed with scanpy downstream analysis. However, I would like to use the X_pca and X_umap values that I imported from my analysis through Seurat.
Here is my code used for converting my SeuratObject to h5ad. I used the code provided by the SEVtras tutorial (there was a code for exporting the PCA and UMAP values from Seurat, there was no code to input the values into the scanpy h5ad object, so I wrote my own for importing PCA and UMAP values).
In conclusion, these are my final questions:
Thanks for your help in advance!