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ventolab / CellphoneDB

CellPhoneDB can be used to search for a particular ligand/receptor, or interrogate your own HUMAN single-cell transcriptomics data.
https://www.cellphonedb.org/
MIT License
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Error when subsetting with selected rows and cols #51

Closed garfieldyc closed 2 years ago

garfieldyc commented 2 years ago

Hi, thank you for developing this wonderful tool. I have encountered an error when trying to dot plot selected rows and cols using the following script. cellphonedb plot dot_plot --rows in/rows.txt --columns in/columns.txt

It showed Error: Invalid value for '--rows': File 'in/rows.txt' does not exist. It seems rows.txt and columns.txt files are not in the correct directory. I am wondering where these two files should be placed.

Thank you,

prete commented 2 years ago

Hi @garfieldyc, thank you for using CellPhoneDB.

Can you confirm if rows.txt and columns.txt are actually inside the in folder you mention?

If you've cloned the repository and you're trying to run the examples keep in mind that the paths for those is in/example_data/ from the base path CellphoneDB where the repository was cloned.

garfieldyc commented 2 years ago

Hi @garfieldyc, thank you for using CellPhoneDB.

Can tou confirm if rows.txt and columns.txt are actually inside the in folder you mention?

If you've cloned the repository and you're trying to run the examples keep in mind that the paths for those is in/example_data/ from the base path CellphoneDB where the repository was cloned.

Thank you for your reply. It works now.