Cannot save to defined path

[spatts14]

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• [x] I have checked that this issue has not already been reported.
• [x] I have confirmed this bug exists on the latest version of scanpy.
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What happened?

Hi,

Apologies if I've missed this addressed somewhere else, however I would like to save my figured to a defined directory. It doesn't seem I can do that without first changing the current working directory outside the line of code.

What is the best way to save my plot to a specific directory without having to change it each time using os.chdir?

I have seen this issue from 2 years ago but wondered if any changes have been made since.

Minimal code sample

output_dir_fig = "chosen/path/to/directory"
sc.pl.highest_expr_genes(adata, n_top=10, save= f"{output_dir_fig}/highest_expr_genes.png")

Error output

---

FileNotFoundError Traceback (most recent call last) Cell In[85], line 1 ----> 1 sc.pl.highest_expr_genes(adata, n_top=10, save= f"{output_dir_fig}/highest_expr_genes.png")

File /opt/anaconda3/envs/scanpy/lib/python3.11/site-packages/legacy_api_wrap/init.py:80, in legacy_api..wrapper..fn_compatible(*args_all, **kw) 77 @wraps(fn) 78 def fn_compatible(*args_all: P.args, **kw: P.kwargs) -> R: 79 if len(args_all) <= n_positional: ---> 80 return fn(*args_all, **kw) 82 args_pos: P.args 83 args_pos, args_rest = args_all[:n_positional], args_all[n_positional:]

File /opt/anaconda3/envs/scanpy/lib/python3.11/site-packages/scanpy/plotting/_qc.py:105, in highest_expr_genes(adata, n_top, show, save, ax, gene_symbols, log, **kwds) 103 ax.set_xscale("log") 104 show = settings.autoshow if show is None else show --> 105 _utils.savefig_or_show("highest_expr_genes", show=show, save=save) 106 if show: 107 return None

File /opt/anaconda3/envs/scanpy/lib/python3.11/site-packages/scanpy/plotting/_utils.py:339, in savefig_or_show(writekey, show, dpi, ext, save) 337 show = settings.autoshow if show is None else show 338 if save: --> 339 savefig(writekey, dpi=dpi, ext=ext) 340 if show: ... -> 2456 fp = builtins.open(filename, "w+b") 2458 try: 2459 save_handler(self, fp, filename)

FileNotFoundError: [Errno 2] No such file or directory: '/Users/sarapatti/Desktop/PhD_projects/Llyod_lab/Col1_scRNAseq/scripts_new/Python_notebooks/figures/highest_expr_genes/Users/sarapatti/Desktop/PhD_projects/Llyod_lab/Col1_scRNAseq/analysis/figures/highest_expr_genes.png' Output is truncated. View as a scrollable element or open in a text editor. Adjust cell output settings...

Versions

scanpy==1.10.1 
anndata==0.10.7 
umap==0.5.5 
numpy==1.26.4 
scipy==1.13.0 
pandas==2.2.2 
scikit-learn==1.4.2 
statsmodels==0.14.1 
igraph==0.11.5 
pynndescent==0.5.12