ctheodoris

/

Geneformer

like 251

Hi,

the documentation of EmbExtractor says:

max_ncells: None, int
Maximum number of cells to extract embeddings from.
Default is 1000 cells randomly sampled from input data.
If None, will extract embeddings from all cells.

But setting max_ncells=None to get all embeddings causes a TypeError:
Traceback (most recent call last):
File "/home/user/gf/src/plot_embeddings.py", line 49, in
args = parse_args()
File "/home/user/gf/src/plot_embeddings.py", line 42, in main
embs = embex.extract_embs(args.model_path,
File "/home/user/gf/src/geneformer/emb_extractor.py", line 840, in plot_embs
if max_ncells_to_plot > self.max_ncells:
TypeError: '>' not supported between instances of 'int' and 'NoneType'

Not sure if this is the right place to post, since huggingface has no issue section.