minor_comment

python/quantmsio/quantms_io/core/statistic.py

@@ -48,6 +48,9 @@ def __init__(self,feature_path:str=None,ibaq_path:str=None):
         self.ibaq_db = self.load_db(ibaq_path)
 
     def load_db(self,path:str):
+        '''
+        Load the database.
+        '''
         if path is not None:
             if os.path.exists(path):
                 if path.endswith(".parquet"):
@@ -62,23 +65,31 @@ def load_db(self,path:str):
 
     @check_exist('feature_db')
     def get_unique_peptides(self):
-
+        '''
+        return: A list of deduplicated peptides.
+        '''
         feature_db = self.feature_db
         unique_peps = duckdb.sql(f"SELECT DISTINCT sequence FROM feature_db").df()
 
         return unique_peps['sequence'].tolist()
 
     @check_exist('ibaq_db')
     def get_unique_proteins(self):
-
+        '''
+        return: A list of deduplicated proteins.
+        '''
         ibaq_db = self.ibaq_db
         unique_prts = duckdb.sql(f"SELECT DISTINCT protein FROM ibaq_db").df()
 
         return unique_prts['protein'].tolist()
 
     @check_exist('feature_db')
     def query_peptide(self,peptide:str):
-
+        '''
+        peptide: Peptide that need to be queried.
+        return: A DataFrame of all information about query peptide.
+        '''
+
         feature_db = self.feature_db
         if check_string('^[A-Z]+$',peptide):
             return duckdb.sql(f"SELECT * FROM feature_db WHERE sequence ='{peptide}'").df()
@@ -87,7 +98,11 @@ def query_peptide(self,peptide:str):
 
     @check_exist('ibaq_db')
     def query_protein(self,protein:str):
-
+        '''
+        protein: Protein that need to be queried.
+        return: A DataFrame of all information about query protein.
+        '''
+
         ibaq_db = self.ibaq_db
         if check_string('^[A-Z]+',protein):
             return duckdb.sql(f"SELECT * FROM ibaq_db WHERE protein ='{protein}'").df()
@@ -96,6 +111,9 @@ def query_protein(self,protein:str):
 
     @check_exist('feature_db')
     def plot_peptide_distribution_of_protein(self):
+        '''
+        Bar graphs of peptide counts for different samples.
+        '''
         feature_db = self.feature_db
         df = duckdb.sql(f"SELECT sample_accession, COUNT(sequence) FROM feature_db GROUP BY sample_accession").df()
         df.columns = ['sample','peptides']
@@ -107,11 +125,14 @@ def plot_peptide_distribution_of_protein(self):
 
     @check_exist('feature_db')
     def plot_intensty_distribution_of_samples(self):
+        '''
+        Kde of peptide intensity distribution for different samples.
+        '''
         feature_db = self.feature_db
         sample_accessions = duckdb.sql(f"SELECT DISTINCT sample_accession FROM feature_db").df()['sample_accession'].tolist()
         random.shuffle(sample_accessions)
-        if len(sample_accessions) > 8:
-            sample_accessions = sample_accessions[:8]
+        if len(sample_accessions) > 10:
+            sample_accessions = sample_accessions[:10]
         df = pd.DataFrame()
         for sample in sample_accessions:
             df_sample = duckdb.sql(f"SELECT intensity FROM feature_db WHERE sample_accession='{sample}'").df()
@@ -124,6 +145,9 @@ def plot_intensty_distribution_of_samples(self):
 
     @check_exist('feature_db')
     def plot_intensty_box_of_samples(self):
+        '''
+        Boxplot of peptide intensity distribution for different samples.
+        '''
         feature_db = self.feature_db
         sample_accessions = duckdb.sql(f"SELECT DISTINCT sample_accession FROM feature_db").df()['sample_accession'].tolist()
         random.shuffle(sample_accessions)