Update default of logo_type in AALogo to 'probability'

Author: breimanntools

aaanalysis/seq_analysis/_aalogo.py

@@ -50,7 +50,7 @@ class AALogo:
     """
 
     def __init__(self,
-                 logo_type: Literal["probability", "weight", "counts", "information"] = "counts"
+                 logo_type: Literal["probability", "weight", "counts", "information"] = "probability"
                  ):
         list_to_type = ["probability", "weight", "counts", "information"]
         ut.check_str_options(name="to_type", val=logo_type, list_str_options=list_to_type)

aaanalysis/seq_analysis/_aalogo_plot.py

@@ -44,15 +44,15 @@ class AALogoPlot:
     """
 
     def __init__(self,
-                 logo_type: Literal["probability", "weight", "counts", "information"] = "counts",
+                 logo_type: Literal["probability", "weight", "counts", "information"] = "probability",
                  jmd_n_len: int = 10,
                  jmd_c_len: int = 10,
                  verbose: bool = True
                  ):
         """
         Parameters
         ----------
-        logo_type : {'probability', 'weight', 'counts', 'information'}, default='counts'
+        logo_type : {'probability', 'weight', 'counts', 'information'}, default='probability'
             Type of sequence logo representation:
 
             - 'probability': Normalized probability distribution of amino acids.