marsilea.plotter.SeqLogo

class SeqLogo(matrix, width=0.9, color_encode=None, stack='descending', **kwargs)

Bases: StatsBase

Sequence logo

Parameters:

matrixpandas.DataFrame

Drawing matrix, the data is the height of logo with columns as positions and rows as nucleotides/amino acids letters.

widthfloat, optional

The width of each letter, by default .9, should be within [0, 1]

color_encodedict, optional

The color encoding for each letter, should be a dict with key as letter and value as color

stack{“descending”, “ascending”, “normal”}, default: “descending”

The stacking order of letters, by height. If normal will stack as the order in matrix.

Examples

>>> import pandas as pd
>>> from marsilea.plotter import SeqLogo
>>> matrix = pd.DataFrame(data=np.random.randint(1, 10, (4, 10)),
...                       index=list("ACGT"))
>>> _, ax = plt.subplots()
>>> colors = {"A": "r", "C": "b", "G": "g", "T": "black"}
>>> SeqLogo(matrix, color_encode=colors).render(ax)

render_main = False