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raphael-group / chisel

CHISEL -- Copy-number Haplotype Inference in Single-cell by Evolutionary Links
BSD 3-Clause "New" or "Revised" License
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Error while plotting! #30

Closed jmfa closed 10 months ago

jmfa commented 1 year ago

Hi,

Thanks for the nice tool. I'm trying to run chisel on a scDNA-seq dataset composed of 26 cells. I've successfully ran all steps of the pipeline but I get an error at the end while plotting:

[2023-Oct-14 14:42:07]Plotting RDR and mirrored BAF plots for 20 random cells in rbplot_mirrored.png Traceback (most recent call last): File "/mnt/netapp2/Store_uni/home/uvi/be/jfa/conda/envs/chisel/lib/python2.7/site-packages/chisel/Plotter.py", line 561, in <module> main() File "/mnt/netapp2/Store_uni/home/uvi/be/jfa/conda/envs/chisel/lib/python2.7/site-packages/chisel/Plotter.py", line 119, in main rbplot_mirrored(bins, chosen, args) File "/mnt/netapp2/Store_uni/home/uvi/be/jfa/conda/envs/chisel/lib/python2.7/site-packages/chisel/Plotter.py", line 296, in rbplot_mirrored g = sns.lmplot(**par) File "/home/uvi/be/jfa/.local/lib/python2.7/site-packages/seaborn/regression.py", line 619, in lmplot facets.map_dataframe(regplot, x, y, **regplot_kws) File "/home/uvi/be/jfa/.local/lib/python2.7/site-packages/seaborn/axisgrid.py", line 834, in map_dataframe self._facet_plot(func, ax, args, kwargs) File "/home/uvi/be/jfa/.local/lib/python2.7/site-packages/seaborn/axisgrid.py", line 852, in _facet_plot func(*plot_args, **plot_kwargs) File "/home/uvi/be/jfa/.local/lib/python2.7/site-packages/seaborn/regression.py", line 812, in regplot x_jitter, y_jitter, color, label) File "/home/uvi/be/jfa/.local/lib/python2.7/site-packages/seaborn/regression.py", line 116, in __init__ self.dropna("x", "y", "units", "x_partial", "y_partial") File "/home/uvi/be/jfa/.local/lib/python2.7/site-packages/seaborn/regression.py", line 68, in dropna setattr(self, var, val[not_na]) IndexError: invalid index to scalar variable.

Any idea of what might be causing this issue? Thanks in advance, J

simozacca commented 10 months ago

You might have not enough cells to generate plots that are done only for a sample of cells; please try to running the plotting with the flag --sample 1 to force to generate these plots only for a single cell. Also, make sure to re-run the cloning step by descreasing the default value of the minimum number of cells per clone, since you have only a few cells (see more info here.

Please feel free to re-open the issue if the problem persists.