Merge pull request #617 from padix-key/color-scheme

Use 'flower' as default color scheme

Author: padix-key

doc/examples/scripts/sequence/misc/color_schemes_protein.py

@@ -9,7 +9,7 @@
     - **clustalx** - Default color scheme of the *ClustalX* software
     - Color schemes generated with the software *Gecos*
       :footcite:`Kunzmann2020`:
-      
+
       - **flower** - Light color scheme, based on *BLOSUM62*
       - **blossom** - Light color scheme with high contrast, based on
         *BLOSUM62*, depicts symbol similarity worse than *flower*
@@ -21,12 +21,12 @@
         scheme, based on *BLOSUM62*
       - **ocean** - Blue shifted, light color scheme, based on
         *BLOSUM62*
-    
+
     - Color schemes adapted from *JalView* :footcite:`Clamp2004`:
-      
+
       - **zappo** - Color scheme that depicts physicochemical properties
       - **taylor** - Color scheme invented by Willie Taylor
-      - **buried** - Color scheme depicting the *buried index* 
+      - **buried** - Color scheme depicting the *buried index*
       - **hydrophobicity** - Color scheme depicting hydrophobicity
       - **prophelix** - Color scheme depicting secondary structure
         propensities
@@ -70,8 +70,8 @@
 # Get color scheme names
 alphabet = seq.ProteinSequence.alphabet
 schemes = [
-    "rainbow", "clustalx",
     "flower", "blossom", "spring", "wither", "autumn", "sunset", "ocean",
+    "rainbow", "clustalx",
     "zappo", "taylor", "buried", "hydrophobicity",
     "prophelix", "propstrand", "propturn"
 ]

src/biotite/sequence/graphics/alignment.py

@@ -310,7 +310,7 @@ class LetterTypePlotter(LetterPlotter):
         The alphabet of the alignment(s) to be plotted
     color_scheme : str or list of (tuple or str), optional
         Either a valid color scheme name
-        (e.g. ``"rainbow"``, ``"clustalx"``, ``blossom``, etc.)
+        (e.g. ``"flower"``, ``"clustalx"``, ``blossom``, etc.)
         or a list of *Matplotlib* compatible colors.
         The list length must be at least as long as the
         length of the alphabet used by the sequences.
@@ -330,7 +330,7 @@ def __init__(self, axes, alphabet, color_scheme=None, color_symbols=False,
         super().__init__(axes, color_symbols, font_size, font_param)
 
         if color_scheme is None:
-            self._colors = get_color_scheme("rainbow", alphabet)
+            self._colors = get_color_scheme("flower", alphabet)
         elif isinstance(color_scheme, str):
             self._colors = get_color_scheme(color_scheme, alphabet)
         else:
@@ -873,7 +873,7 @@ def plot_alignment_type_based(axes, alignment, symbols_per_line=50,
         is equal to the size of a symbol box.
     color_scheme : str or list of (tuple or str), optional
         Either a valid color scheme name
-        (e.g. ``"rainbow"``, ``"clustalx"``, ``blossom``, etc.)
+        (e.g. ``"flower"``, ``"clustalx"``, ``blossom``, etc.)
         or a list of *Matplotlib* compatible colors.
         The list length must be at least as long as the
         length of the alphabet used by the sequences.

src/biotite/sequence/graphics/logo.py

@@ -36,16 +36,16 @@ def plot_sequence_logo(axes, profile, scheme=None, **kwargs):
         The logo is created based on this profile.
     scheme : str or list of (tuple or str)
         Either a valid color scheme name
-        (e.g. ``"rainbow"``, ``"clustalx"``, ``blossom``, etc.)
+        (e.g. ``"flower"``, ``"clustalx"``, ``blossom``, etc.)
         or a list of *Matplotlib* compatible colors.
         The list length must be at least as long as the
         length of the alphabet used by the `profile`.
     **kwargs
         Additional `text parameters <https://matplotlib.org/api/text_api.html#matplotlib.text.Text>`_.
-    
+
     References
     ----------
-    
+
     .. footbibliography::
     """
     from matplotlib.text import Text
@@ -59,16 +59,16 @@ def plot_sequence_logo(axes, profile, scheme=None, **kwargs):
         raise TypeError("The sequences' alphabet must be a letter alphabet")
 
     if scheme is None:
-        colors = get_color_scheme("rainbow", alphabet)
+        colors = get_color_scheme("flower", alphabet)
     elif isinstance(scheme, str):
         colors = get_color_scheme(scheme, alphabet)
     else:
         colors = scheme
-    
+
     # 'color' and 'size' property is not passed on to text
     kwargs.pop("color", None)
     kwargs.pop("size",  None)
-    
+
     frequencies, entropies, max_entropy = _get_entropy(profile)
     stack_heights = (max_entropy - entropies)
     symbols_heights = stack_heights[:, np.newaxis] * frequencies