remove the last chunk from T1_Method2.ipynb and T1_Method3.ipynb

[fentouxungui]

change 1

the last chunk from T1_Method2.ipynb and T1_Method3.ipynb files should be removed :

from cellphonedb.src.core.methods import cpdb_statistical_analysis_method

cpdb_results = cpdb_statistical_analysis_method.call(
    cpdb_file_path = cpdb_file_path,                 
    meta_file_path = meta_file_path,                 
    counts_file_path = counts_file_path,             
    counts_data = 'hgnc_symbol',                     
    iterations = 1000,                               
    threshold = 0.1,                                 
    threads = 5,                                     
    debug_seed = 42,                                 
    result_precision = 3,                            
    pvalue = 0.05,                                   
    separator = '|',                                
    debug = False,                                   
    output_path = out_path,                          
    output_suffix = None                             

    active_tfs_file_path = active_tf_path,           # optional: defines cell types and their active TFs.
    microenvs_file_path = microenvs_file_path,       # optional (default: None): defines cells per microenvironment.
    score_interactions = True,                       # optional: whether to score interactions or not. 

    subsampling = False,                            
    subsampling_log = False,                         
    subsampling_num_pc = 100,                        
    subsampling_num_cells = 1000,                   
    e  (default: None).
    )

change 2

for T1_Method3.ipynb file: change /home/jovyan/cpdb_tutorial/data/normalised_log_counts.h5ad to counts_file_path

[datasome]

Hi fentouxungui,

Many thanks for spotting these and letting us know - much appreciated! I have fixed both - see e.g. https://github.com/ventolab/CellphoneDB/blob/master/notebooks/T1_Method3.ipynb

Best,

Robert.