datasome
commented
8 months ago Hi Rich,
Thank you for reaching out and for using CellphoneDB and CellphoneDB Viz.
Yes, CellphoneDB Viz is currently less flexible on column naming than CellphoneDB - I will try to improve it in time. The lack of cluster column in your DEGs.txt file was indeed the first problem you faced. One other thing to check is if you're providing a microenvironments file, it should contain columns: microenvironment and _celltype. If you still get errors, please could you include them in your message and I will comment. Many thanks.
Best,
Robert.
Hello,
I successfully ran CellphoneDB using the DEG method, and now I am trying to use the CellphoneDB_Viz Docker container. I keep getting a KeyError: 'cluster' error when loading the project. My column name in the DEGs.txt file is "cell_type" (which was how the jupyter notebook example was labeled), but I noticed that the celltype column of the degs_in_epithelials.tsv DEGs file (provided in the config.yml) was labeled "cluster". Could this be the issue? I changed the column name to 'cluster' in my DEGs file and recreated the Docker image, but this introduced new indexing errors. Could I get some assistance on how to proceed? Thanks.
Rich