Find gene symbols exist only in .raw attribute #962
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This change fixed issues of plotting gene symbols which exist only in .raw attribute of AnnData object.
Find gene symbols exist only in .raw attribute
ivirshup
requested changes
Feb 5, 2020
Comment on lines
+2988
to
+3019
| # translate gene_symbols to var_names | ||
| # slow method but gives a meaningful error if no gene symbol is found: | ||
| if use_raw: | ||
| if gene_symbols is not None and gene_symbols in adata.raw.var.columns: | ||
| translated_var_names = [] | ||
| for symbol in var_names: | ||
| if symbol not in adata.raw.var[gene_symbols].values: | ||
| logg.error( | ||
| f"Gene symbol {symbol!r} not found in given " | ||
| f"gene_symbols column: {gene_symbols!r}" | ||
| ) | ||
| return | ||
| translated_var_names.append( | ||
| adata.raw.var[adata.raw.var[gene_symbols] == symbol].index[0] | ||
| ) | ||
| return | ||
| translated_var_names.append( | ||
| adata.var[adata.var[gene_symbols] == symbol].index[0] | ||
| ) | ||
| symbols = var_names | ||
| var_names = translated_var_names | ||
| symbols = var_names | ||
| var_names = translated_var_names | ||
| else: | ||
| if gene_symbols is not None and gene_symbols in adata.var.columns: | ||
| translated_var_names = [] | ||
| for symbol in var_names: | ||
| if symbol not in adata.var[gene_symbols].values: | ||
| logg.error( | ||
| f"Gene symbol {symbol!r} not found in given " | ||
| f"gene_symbols column: {gene_symbols!r}" | ||
| ) | ||
| return | ||
| translated_var_names.append( | ||
| adata.var[adata.var[gene_symbols] == symbol].index[0] | ||
| ) | ||
| symbols = var_names | ||
| var_names = translated_var_names |
There was a problem hiding this comment.
How about using sc.get.obs_df for this? I believe it already has the logic you're implementing.
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This change fixed an issue of retrieving data for gene symbols which exist only in the .raw attribute of an AnnData object.