Custom-height letters

[gezmi]

Hi!

This is a great package and I would definitely use it a lot. I have a question: is there any way to provide custom-height metric to sequence logos? Like in the ggseqlogo package in R, where the letters can even have negative height for depletion: https://omarwagih.github.io/ggseqlogo/#custom-height_logos

Thank you!

[padix-key]

Hi, unfortunately there is currently no way to provide custom heights to symbols in a sequence logo.
The only way is modifying the symbols attribute in the input SequenceProfile, but this does not allow for negative heights.

However, the source code of the actual plotting is quite short, if you are willing to implement the use case yourself:

biotite/src/biotite/sequence/graphics/logo.py

Lines 9 to 97 in ef16ea9

	import numpy as np
	from ...visualize import set_font_size_in_coord
	from ..alphabet import LetterAlphabet
	from .colorschemes import get_color_scheme
	import warnings
	from ..align import Alignment
	from .. import SequenceProfile
	def plot_sequence_logo(axes, profile, scheme=None, **kwargs):
	"""
	Create a sequence logo. :footcite:`Schneider1990`
	A sequence logo is visualizes the positional composition and
	conservation of a profile encoded in the size of the letters.
	Each position displays all symbols that are occurring at this
	position stacked on each other, with their relative heights depicting
	their relative frequency.
	The height of such a stack depicts its conservation.
	It is the maximum possible Shannon entropy of the alphabet
	subtracted by the positional entropy.
	Parameters
	----------
	axes : Axes
	The axes to draw the logo one.
	profile: SequenceProfile
	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.)
	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
	if isinstance(profile, Alignment):
	warnings.warn("Using an alignment for this method is deprecated; use a profile instead", DeprecationWarning)
	profile = SequenceProfile.from_alignment(profile)
	alphabet = profile.alphabet
	if not isinstance(alphabet, LetterAlphabet):
	raise TypeError("The sequences' alphabet must be a letter alphabet")
	if scheme is None:
	colors = get_color_scheme("rainbow", 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
	index_order = np.argsort(symbols_heights, axis=1)
	for i in range(symbols_heights.shape[0]):
	# Iterate over the alignment columns
	index_order = np.argsort(symbols_heights)
	start_height = 0
	for j in index_order[i]:
	# Stack the symbols at position on top of the preceeding one
	height = symbols_heights[i,j]
	if height > 0:
	symbol = alphabet.decode(j)
	text = axes.text(
	i+0.5, start_height, symbol,
	ha="left", va="bottom", color=colors[j],
	# Best results are obtained with this font size
	size=1,
	**kwargs
	)
	text.set_clip_on(True)
	set_font_size_in_coord(text, width=1, height=height)
	start_height += height
	axes.set_xlim(0.5, len(profile.symbols)+0.5)
	axes.set_ylim(0, max_entropy)

symbol_heights and start_height are the variables you are looking for.

I will keep this issue open, since I think custom heights are a useful feature to have.