hchen725 commited on
Commit
4c0377b
1 Parent(s): 8aee0ff

Update geneformer/emb_extractor.py

Browse files

Update UMAP plotting to appropriately save figure in specified output directory

Files changed (1) hide show
  1. geneformer/emb_extractor.py +4 -2
geneformer/emb_extractor.py CHANGED
@@ -270,7 +270,9 @@ def plot_umap(embs_df, emb_dims, label, output_file, kwargs_dict):
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  if kwargs_dict is not None:
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  default_kwargs_dict.update(kwargs_dict)
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- sc.pl.umap(adata, color=label, save=output_file, **default_kwargs_dict)
 
 
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  def gen_heatmap_class_colors(labels, df):
@@ -783,7 +785,7 @@ class EmbExtractor:
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  output_file = (
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  Path(output_directory) / output_prefix_label
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  ).with_suffix(".pdf")
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- plot_umap(embs, emb_dims, label, output_prefix_label, kwargs_dict)
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  if plot_style == "heatmap":
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  for label in self.labels_to_plot:
 
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  if kwargs_dict is not None:
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  default_kwargs_dict.update(kwargs_dict)
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+ with plt.rc_context():
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+ sc.pl.umap(adata, color=label, **default_kwargs_dict)
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+ plt.savefig(output_file, bbox_inches="tight")
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  def gen_heatmap_class_colors(labels, df):
 
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  output_file = (
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  Path(output_directory) / output_prefix_label
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  ).with_suffix(".pdf")
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+ plot_umap(embs, emb_dims, label, output_file, kwargs_dict)
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  if plot_style == "heatmap":
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  for label in self.labels_to_plot: