Transfer adata format to dataframe

[chen-peng-1874]

Dear GuangyuWangLab members,

Another question is about data transfer. I have generated adata for "scvelo" analysis, which has columns of "seurat_cluster" and U_map embeddings. As I noticed that the syntax in your celldancer website, there is a sentence for gene list, as shown below:

cdutil.adata_to_df_with_embed(adata,
                              us_para=['Mu','Ms'],
                              cell_type_para='celltype',
                              embed_para='X_umap',
                              save_path='cell_type_u_s.csv',
                              **_gene_list=['Hba-x','Smim1']_**)

What if I want all the genes listed? Thank you!

[Abclisy]

If in your adata, the 'seurat_cluster' is one column of adata.obs, 'X_umap' is one element of adata.obsm, you can use the codes below to transfer all genes.

cdutil.adata_to_df_with_embed(adata,
                              us_para=['Mu','Ms'],
                              cell_type_para='seurat_cluster',
                              embed_para='X_umap',
                              save_path='cell_type_u_s.csv')

Not inputting the gene_list will let adata_to_df_with_embed defaults get all genes.

[chen-peng-1874]

If in your adata, the 'seurat_cluster' is one column of adata.obs, 'X_umap' is one element of adata.obsm, you can use the codes below to transfer all genes.

cdutil.adata_to_df_with_embed(adata,
                              us_para=['Mu','Ms'],
                              cell_type_para='seurat_cluster',
                              embed_para='X_umap',
                              save_path='cell_type_u_s.csv')

Not inputting the gene_list will let adata_to_df_with_embed defaults get all genes.

Thank you, Abclisy! I'll have a try.

[zhijunyuu]

Hey cellDancer group,

Thanks for the nice tool! I have the adata as follows:

AnnData object with n_obs × n_vars = 23496 × 18964
    obs: 'orig.ident', 'nCount_RNA', 'nFeature_RNA', 'donor_id', 'prob_max', 'prob_doublet', 'n_vars', 'best_singlet', 'doublet_logLikRatio', 'nCount_SCT', 'nFeature_SCT', 'pANN', 'gender', 'location', 'donors', 'SCT_snn_res.0.5', 'seurat_clusters', 'S.Score', 'G2M.Score', 'Phase', 'old.ident', 'RNA_snn_res.0.4', 'cell_types', 'batch', 'initial_size_unspliced', 'initial_size_spliced', 'initial_size'
    var: 'name', 'Accession', 'Chromosome', 'End', 'Start', 'Strand'
    uns: 'cell_types_colors'
    obsm: 'X_harmony', 'X_pca', 'X_umap'
    layers: 'ambiguous', 'matrix', 'spliced', 'unspliced'

and I was using the adata_to_df_with_embed function to transfer adata into dataframe with the code as below:

cdutil.adata_to_df_with_embed(adata,
                              us_para=['spliced','unspliced'],
                              cell_type_para='cell_types',
                              embed_para='X_umap',
                              save_path='cell_type_u_s.csv')

But I got an error: ValueError: If using all scalar values, you must pass an index Do you have any idea about this error? Thanks in advance!

Best, Zhijun

[chen-peng-1874]

It seems that you don't have "Mu" and "Ms" in your obsm.

You can process the data in scvelo, and then use cdutil.

Hope that will help you.

---

From: zhijunyuu @.> Sent: Wednesday, April 26, 2023 2:10 AM To: GuangyuWangLab2021/cellDancer @.> Cc: Peng Chen @.>; State change @.> Subject: Re: [GuangyuWangLab2021/cellDancer] Transfer adata format to dataframe (Issue #4)

Hey cellDancer group,

Thanks for the nice tool! I have the adata as follows: AnnData object with n_obs × n_vars = 23496 × 18964 obs: 'orig.ident', 'nCount_RNA', 'nFeature_RNA', 'donor_id', 'prob_max', 'prob_doublet', 'n_vars', 'best_singlet', 'doublet_logLikRatio', 'nCount_SCT', 'nFeature_SCT', 'pANN', 'gender', 'location', 'donors', 'SCT_snn_res.0.5', 'seurat_clusters', 'S.Score', 'G2M.Score', 'Phase', 'old.ident', 'RNA_snn_res.0.4', 'cell_types', 'batch', 'initial_size_unspliced', 'initial_size_spliced', 'initial_size' var: 'name', 'Accession', 'Chromosome', 'End', 'Start', 'Strand' uns: 'cell_types_colors' obsm: 'X_harmony', 'X_pca', 'X_umap' layers: 'ambiguous', 'matrix', 'spliced', 'unspliced'

and I was using the adata_to_df_with_embed function to transfer adata into dataframe with the code as below: cdutil.adata_to_df_with_embed(adata, us_para=['spliced','unspliced'], cell_type_para='cell_types', embed_para='X_umap', save_path='cell_type_u_s.csv')

But I got an error: ValueError: If using all scalar values, you must pass an index Do you have any idea about this error? Thanks in advance!

Best, Zhijun

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[Abclisy]

Hi zhijunyuu, the codes below will help you to get the 'Mu' and 'Ms' in your 'layers' of adata.

# !pip install scvelo --upgrade --quiet
import scvelo as scv
scv.pp.filter_and_normalize(adata, min_shared_counts=20, n_top_genes=2000)
scv.pp.moments(adata, n_pcs=30, n_neighbors=30)

scv.pp.filter_and_normalize runs the following:

scv.pp.filter_genes(adata, min_shared_counts=20)
scv.pp.normalize_per_cell(adata)
scv.pp.filter_genes_dispersion(adata, n_top_genes=2000)
scv.pp.log1p(adata)

For more information, Data Preparation might be helpful. We will add more details about preprocessing on our website later. If it still does not work, could you send us a small subset of your data to let us repeat and debug if possible? Thank you!