fix

diann_lib_processing.py

@@ -95,7 +95,7 @@ def predict(data_pred, model, output_path):
 
 
 if __name__ =='__main__':
-    df = load_lib('spectral_lib/first_lib.parquet')
+    # df = load_lib('spectral_lib/first_lib.parquet')
 
     # plt.hist(df['RT'])
     # plt.savefig('test.png')

identification/result_extraction.py

@@ -3,7 +3,7 @@ import pandas as pd
 from matplotlib_venn import venn2
 import matplotlib.pyplot as plt
 
-def compare_id(path_1,path_2):
+def compare_id(path_1,path_2,sample_name):
     df_1 = pd.read_csv(path_1, sep='\t', encoding='latin-1')
     df_2 = pd.read_csv(path_2, sep='\t', encoding='latin-1')
     peptides_1 = set(df_1['Stripped.Sequence'].tolist())
@@ -11,7 +11,13 @@ def compare_id(path_1,path_2):
     peptides_2 = set(df_2['Stripped.Sequence'].tolist())
     protein_2 = set(df_2['Protein.Ids'].tolist())
 
-    venn2((peptides_1, peptides_2), ('custom lib', 'base lib')) # venn2 works for two sets
-    plt.savefig('venn_diag.png')
+    venn2((peptides_1, peptides_2), ('custom lib', 'base lib'), set_colors=('g','r')) # venn2 works for two sets
+    plt.title('Peptide identifications on {} sample'.format(sample_name))
+    plt.savefig('venn_diag_pep_{}.png'.format(sample_name))
 
-compare_id('CITFRE_ANA_69/report_custom.tsv','CITFRE_ANA_69/report_first_lib.tsv')
+    plt.clf()
+    venn2((protein_1, protein_2), ('custom lib', 'base lib'), set_colors=('g','r')) # venn2 works for two sets
+    plt.title('Protein identifications on {} sample'.format(sample_name))
+    plt.savefig('venn_diag_prot_{}.png'.format(sample_name))
+
+compare_id('CITFRE_ANA_69/report_custom.tsv','CITFRE_ANA_69/report_first_lib.tsv',sample_name='CITFRE_ANA_69')