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c2c.analysis.run_tensor_cell2cell_pipeline #58
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Hi! It could be due to the version of matplotlib you are using. Which version are you using? I recommend using v.3.7.3. Also, if you are using plotnine in combination with matplotlib (for example when using LIANA), I know that importing plotnine also messes up the plots from tensor-cell2cell. |
Hi! Quick question, which python version and cell2cell version are you using? You might need creating a new environment with proper versions I think. This could be a good starting point: https://github.com/saezlab/ccc_protocols/tree/main/env_setup |
Hi!Thank you for your reply!My python version is 3.9, and my cell2cell version is 0.6.4. I have seen that python is 3.10 on this website, and the versions of some other packages have been updated. I am trying the new environment, because the GPU I use has some problems when installing cuda, and I am trying to solve the problem to see if it can be successful. |
I think before trying a new environment you should try updating cell2cell to the latest version (0.7.4), the legend issue was solved in v0.7.0 (see notes here). I think you are having this issue because your version is v0.6.4 |
Hi!Thank you very much for your answer, this legend problem has been solved! However, I still have a small problem. When I installed cell2cell version 0.7.4, the pands version showed that it should be automatically updated to the new version, but when I ran your example at the beginning, there was a tensor decomposition error. Then I read your answer and set pands version to 1.3.5 to solve this problem. But now if I use cell2cell as the new version, does the pands version need to be updated? Looking forward to your reply! |
Can you show me what error you get with the new pandas version? I could generate a quick fix for that to allow compatibility. Anyways, I don't think you need to update pandas if you don't want to do it. Also, pandas 1.5.1 could be a newer and safer version to use. |
Oh this issue shouldn't happen with the latest version of cell2cell, it was already fixed :) so feel free to update pandas if you want |
Thank you very much for your answer, which is very helpful to me! |
Looks like you data have duplicated gene names. You could try using |
Hello, I have tried this operation and the results show that there are no duplicate gene names and no null values. Then I will nan of adata. X are replaced by 0.But still an error that pandas. Errors. InvalidIndexError: Reindexing only valid with uniquely valued Index objects. I'm very upset and I don't know what's wrong with it? What else do you think might be the problem? Or is the source of the error related to the version of these packages being used? Do I need to set up a specific version or a newer version?What is the main package version you used? Hope to get your answer! Thanks ! |
Hello,I updated the version of liana to 1.3.0 and the error was resolved!Thank you for your kind reply! |
Hello,
When I used your tool to analyze my data, I found that the graph of tensor decomposition I ran out had no legend, so I couldn't get which color represented which cell. How did you get the legend then?
Hope to get your answer!
Thanks !
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