plot_sequence_logo#
- biotite.sequence.graphics.plot_sequence_logo(axes, profile, scheme=None, **kwargs)[source]#
Create a sequence logo. [1]
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:
- axesAxes
The axes to draw the logo one.
- profileSequenceProfile
The logo is created based on this profile.
- schemestr or list of (tuple or str)
Either a valid color scheme name (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 parameters for the
matplotlib.font_manager.FontPropertiesof the text or the createdmatplotlib.patches.PathPatch.
References
Gallery#
Identification of a binding site by sequence conservation