dragonn.plot module

class dragonn.plot.Polygon(context)

Bases: object

exterior

geom_type

interiors

dragonn.plot.PolygonPatch(polygon, **kwargs)

Constructs a matplotlib patch from a geometric object

The polygon may be a Shapely or GeoJSON-like object with or without holes. The kwargs are those supported by the matplotlib.patches.Polygon class constructor. Returns an instance of matplotlib.patches.PathPatch.

Example (using Shapely Point and a matplotlib axes):

>>> b = Point(0, 0).buffer(1.0)
>>> patch = PolygonPatch(b, fc='blue', ec='blue', alpha=0.5)
>>> axis.add_patch(patch)

dragonn.plot.PolygonPath(polygon)

Constructs a compound matplotlib path from a Shapely or GeoJSON-like geometric object

dragonn.plot.add_letter_to_axis(ax, let, x, y, height)

Add ‘let’ with position x,y and height height to matplotlib axis ‘ax’.

dragonn.plot.add_letters_to_axis(ax, letter_heights)

Plots letter on user-specified axis.

ax : axis letter_heights: Nx4 array

dragonn.plot.plot_bases(letter_heights, figsize=(12, 6), ylab='bits')

Plot the N letters with heights taken from the Nx4 matrix letter_heights.

letter_heights: Nx4 array ylab: y axis label

pyplot figure

dragonn.plot.plot_motif(motif_name, figsize, ylab='bits', information_content=True)

Plot motifs from encode motifs file

dragonn.plot.plot_pwm(letter_heights, figsize=(12, 6), ylab='bits', information_content=True)

Plots pwm. Displays information content by default.

dragonn.plot.standardize_polygons_str(data_str)

Given a POLYGON string, standardize the coordinates to a 1x1 grid.

Input : data_str (taken from above) Output: tuple of polygon objects