I was trying to run the DEG-based method with the microenvironments file but it failed with the following error:
Exception: Some clusters/cell_types in DEGs are not present in metadata.
I am currently using the example dataset provided here:
https://github.com/ventolab/CellphoneDB/tree/master/example_data
The commands I am using are:
from cellphonedb.src.core.methods import cpdb_degs_analysis_method
deconvoluted, means, relevant_interactions, significant_means = cpdb_degs_analysis_method.call( cpdb_file_path = '/media/user/disk31/cellphoneDB/v4.1.0/cellphonedb.zip', meta_file_path = '/media/user/disk31/cellphoneDB/CellphoneDB-master/example_data/test_meta.txt', counts_file_path = '/media/user/disk31/cellphoneDB/CellphoneDB-master/example_data/test.h5ad', counts_data = 'hgnc_symbol', degs_file_path = '/media/user/disk31/cellphoneDB/CellphoneDB-master/example_data/test_degs.txt', microenvs_file_path = '/media/user/disk31/cellphoneDB/CellphoneDB-master/example_data/test_microenviroments.txt', output_path = '/media/user/disk31/cellphoneDB/')
Please let me know what I am doing wrong.
ktroule
commented
1 year ago
Hi @ktroule,
I was trying to run the DEG-based method with the microenvironments file but it failed with the following error: Exception: Some clusters/cell_types in DEGs are not present in metadata.
I am currently using the example dataset provided here: https://github.com/ventolab/CellphoneDB/tree/master/example_data The commands I am using are: from cellphonedb.src.core.methods import cpdb_degs_analysis_method
deconvoluted, means, relevant_interactions, significant_means = cpdb_degs_analysis_method.call( cpdb_file_path = '/media/user/disk31/cellphoneDB/v4.1.0/cellphonedb.zip', meta_file_path = '/media/user/disk31/cellphoneDB/CellphoneDB-master/example_data/test_meta.txt', counts_file_path = '/media/user/disk31/cellphoneDB/CellphoneDB-master/example_data/test.h5ad', counts_data = 'hgnc_symbol', degs_file_path = '/media/user/disk31/cellphoneDB/CellphoneDB-master/example_data/test_degs.txt', microenvs_file_path = '/media/user/disk31/cellphoneDB/CellphoneDB-master/example_data/test_microenviroments.txt', output_path = '/media/user/disk31/cellphoneDB/')Please let me know what I am doing wrong.