Closed tAndreani closed 4 years ago
Hi! I'm not sure what the issue is, but from the traceback it seems like it could have something to do with seaborn. Seaborn depends on the module statsmodels, which if updated through other packages may cause problems in Seaborn. Could you please check if your statsmodels version is 0.8.0? If not, please try the following to uninstall statsmodels and install again:
conda uninstall statsmodels --yes conda install -c taugspurger statsmodels=0.8.0
Hi!
thank you for the quick reply. I have solved the problem now thanks.
Can I ask you a question about the output of --infer_lineage? What are the numbers in the edges and what are the number inside the circles? Are the first "number of sequences" and the second "number of single cells"?
In few words in this plot you provide: https://github.com/Teichlab/bracer/blob/master/test_data/expected_summary/lineage_trees/1.pdf to what correspond the numbers of 10, 22 and 17? These are shared sequences between the inferred clonotype and the cells? Or are these mutations?
..explanation is here: https://cran.r-project.org/web/packages/alakazam/vignettes/Lineage-Vignette.pdf and it seems that: "The igraph graph object will contain clone annotations as graph attributes, sequence annotations as vertex attributes, and mutations along edges as edge attributes. "
Thank you for any reply. Best
Hello,
I would like to infer the lineage tree of my clones (around 140 single B-cells). I have tried to run the summarize command and infer the lineage like:
The summarized plot are presents but it failed to reconstruct the lineage and also to build the network files because the bmp format is not recognized. I have also tried jpeg but had the same problem. This is the error:
at the same time if I run the test example and i ask to summarize and draw the lineage tree using:
I still have the problem of building the network and the lineage tree and this is the error
in the folder there are only these files:
What could be the problem? Any idea?