ZeroDivisionError: integer division or modulo by zero

[simonekats]

masks = palantir.presults.select_branch_cells(adata, eps=0) plt.show()

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ZeroDivisionError Traceback (most recent call last) Cell In[545], line 1 ----> 1 masks = palantir.presults.select_branch_cells(adata, eps=0) 2 plt.show()

File ~/anaconda3/lib/python3.10/site-packages/palantir/presults.py:555, in select_branch_cells(ad, pseudo_time_key, fate_prob_key, q, eps, masks_key, save_as_df) 552 n = fate_probs.shape[0] 554 step = n // PSEUDOTIME_RES --> 555 nsteps = n // step 556 for i in range(nsteps): 557 l, r = i step, (i + 1) step

ZeroDivisionError: integer division or modulo by zero

[katosh]

Hi @simonekats,

Thank you for reporting. My guess is that your dataset has a very small number of cells (<500). The best solution would be to increase the number of cells in tour dataset, as results for such a small sample size might vary. As a quick fix to make this work for the given dataset you can run

palantir.presults.PSEUDOTIME_RES = ad.n_obs

before running the selection. I also made a patch that should avoid this error in the future. You can install the patched version now with

pip install --ignore-installed --no-deps 'git+https://github.com/dpeerlab/Palantir'

Please let me know if the issue persist or if we can close this.

[simonekats]

The first code solved it thank you so much!