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Teichlab / cellphonedb

MIT License
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dot_plot issue #181

Open simonuoft opened 4 years ago

simonuoft commented 4 years ago

Hi, I'm trying to plot the results of a cellphoneDB analysis and I have an error : Segmentation fault: 11.

Does anyone have an idea of where it can come from and how to fix it ? Thanks.

LucasES1 commented 3 years ago

@simonuoft Did you solve this? I have the same issue (with both dot_plot and heatmap_plot). Thanks.

Hi, I'm trying to plot the results of a cellphoneDB analysis and I have an error : Segmentation fault: 11.

Does anyone have an idea of where it can come from and how to fix it ? Thanks.

prete commented 3 years ago

HI @LucasES1 could you please provide CellPhoneDB, operating system and R version?

Do you get anything else from cellphone output or just Segmentation fault: 11? it's possible that your system is running out of memory when trying to execute plotting code.

LucasES1 commented 3 years ago

Hi @prete I'm using CellPhoneDB 2.1.7 (installed this morning), R 3.6.3 (with ggplot2 and pheatmap installed), and MacOS 10.14.6 Mojave The full message that returns is: /Users/myusername/opt/anaconda3/envs/cpdb/lib/python3.7/site-packages/sklearn/utils/deprecation.py:144: FutureWarning: The sklearn.cluster.kmeans module is deprecated in version 0.22 and will be removed in version 0.24. The corresponding classes / functions should instead be imported from sklearn.cluster. Anything that cannot be imported from sklearn.cluster is now part of the private API. warnings.warn(message, FutureWarning) Segmentation fault: 11

Appreciate your insight! I'm pretty new to this.

prete commented 3 years ago

Possibly memory exhausting error. Does this happen to you with the example data (test_meta and test_count)?

You can try running the plotting scripts manually as described here.

LucasES1 commented 3 years ago

I get the same message with the example data as well as my own. I will give a try to running the plots manually, thanks!

flywithiy commented 3 years ago

Hi, I'm trying to plot the results of the cellphonedb_example_data analysis and I have an error :

cpdb-venv/lib/python3.8/site-packages/sklearn/utils/deprecation.py:144: FutureWarning: The sklearn.cluster.kmeans module is deprecated in version 0.22 and will be removed in version 0.24. The corresponding classes / functions should instead be imported from sklearn.cluster. Anything that cannot be imported from sklearn.cluster is now part of the private API. warnings.warn(message, FutureWarning) Does anyone have an idea how to fix it ? Thanks.

prete commented 3 years ago

Hi @flywithiy, thank you for using CellPhoneDB. As explained in this issue, the FutureWarning is not an error but a notification and does not have anything to do with plotting. If you're having issues while plotting I recommend:

If none of those work, could you provide more information about why you consider that to be an error?