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Teichlab / cellphonedb

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Error: Invalid value for "--columns": Path "in/columns.txt" does not exist. #294

Closed aliciahillturner closed 3 years ago

aliciahillturner commented 3 years ago

I am trying to run the command using the below code provided: cellphonedb plot dot_plot --columns in/columns.txt

I can run and generate the total dot plot fine (see here), however when I try to say " --columns in/columns.txt" I get the error "Error: Invalid value for "--columns": Path "in/columns.txt" does not exist." I am not sure if this is a path error or a cellphoneDB error, but my columns.txt file (linked here) is in the same directory as my other files and has the correct information. I am also running this on Linux not sure if that matters?

My goal is to look at the interactions between specific clusters (i.e Macrophage1|Ductal1) but I keep running into this error!

prete commented 3 years ago

The error says that Path "in/columns.txt" does not exist., are you sure that path is correct? May be your columns.txt file lives in the same folder that you're running the plotting command from, in that case it should be cellphonedb plot dot_plot --columns columns.txt

aliciahillturner commented 3 years ago

thank you! It worked :)