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Find gene symbols exist only in .raw attribute #962

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Find gene symbols exist only in .raw attribute #962

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Find gene symbols exist only in .raw attribute
mw201608 Dec 26, 2019
a3a6d44
Merge pull request #1 from mw201608/mw201608-patch-1
mw201608 Dec 26, 2019
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46 changes: 31 additions & 15 deletions scanpy/plotting/_anndata.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2985,22 +2985,38 @@ def _prepare_dataframe(
f'Given {groupby}, valid observations: {adata.obs_keys()}'
)

if gene_symbols is not None and gene_symbols in adata.var.columns:
# translate gene_symbols to var_names
# slow method but gives a meaningful error if no gene symbol is found:
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}"
# 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
Comment on lines +2988 to +3019
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How about using sc.get.obs_df for this? I believe it already has the logic you're implementing.

if layer is not None:
if layer not in adata.layers.keys():
raise KeyError(
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