import numpy as np
from copy import deepcopy
from .tools import updated_dict
[docs]class Band:
"""A band in a migration pattern.
This class controls all visual aspects of the band (form, color, label...).
Parameters
----------
dna_size
migration_distance
Observed migration distance of the band. Useful if you are using this
band to define a ladder, otherwise keep to None.
ladder
Ladder used to determine the migration distance of the band, if no
``migration_distance`` was provided.
band_color
Color of the band. Can be a color name (like 'black', 'red'...) or
an hexadecimal code like '#001aff' (this format is mandatory if you
want to export to browser-based display.
band_thickness
Thickness of the band in pixels.
band_width
Proportion of the column width that is occupied by the band (the columns
for each band pattern have a width of 1.0).
label
Label to be printed on the band, if any provided. Set to '=size' for
printing the band sizes.
label_fontdict
A dict indicating the format of the label if any provided. For instance
``{'size': 7, 'weight':'bold', 'color': '#0011aa'}``.
html
Html appearing when hovering the band.
"""
def __init__(
self,
dna_size,
migration_distance=None,
ladder=None,
band_color="#000000",
band_thickness=2,
band_width=0.7,
label=None,
label_fontdict=None,
html=None,
):
self.dna_size = dna_size
if ladder is not None:
migration_distance = ladder.dna_size_to_migration(dna_size)
self.migration_distance = migration_distance
self.band_color = band_color
self.band_width = band_width
self.band_thickness = band_thickness
self.label = label
self.label_fontdict = label_fontdict
self.html = html
self.initialize()
def initialize(self):
if self.label == "=size":
self.label = self._format_dna_size(self.dna_size)
@staticmethod
def _format_dna_size(dna_size):
"""Prettify the fragment size label, e.g. '13278' becomes '13.3k'"""
if dna_size >= 1000:
kilobases = np.round(dna_size / 1000.0, 1)
number_fmt = "%d" if (kilobases == int(kilobases)) else "%.1f"
return (number_fmt % kilobases) + "k"
else:
return "%d" % dna_size
def _plot_band(self, ax, x_coord):
"""Plot the band's line on the matplotlib ax at the x-coordinate."""
ax.plot(
[x_coord - self.band_width / 2.0, x_coord + self.band_width / 2.0],
[-self.migration_distance, -self.migration_distance],
lw=self.band_thickness,
c=self.band_color,
)
def _plot_label(self, ax, x_coord):
"""Plot the label on (top of) the band."""
if self.label is None:
return
fontdict = updated_dict(
{"color": "white", "family": "sans-serif", "weight": "bold", "size": 10},
self.label_fontdict,
)
ax.text(
x_coord,
-self.migration_distance,
self.label,
horizontalalignment="center",
verticalalignment="center",
fontdict=fontdict,
transform=ax.transData,
bbox=dict(boxstyle="round", fc=self.band_color, lw=0),
)
[docs] def plot(self, ax, x_coord):
"""Plot the band's line and label on the ax at the x-coordinate."""
self._plot_band(ax, x_coord)
self._plot_label(ax, x_coord)
[docs] def to_json(self, ladder=None):
"""Return a dictionary version of the band (for bokeh plotting)."""
return {
prop: self.__dict__[prop]
for prop in [
"dna_size",
"band_color",
"band_width",
"band_thickness",
"label",
"html",
"migration_distance",
]
}
[docs] def modified(self, **attributes):
"""Return a new version of this band, with modified attributes."""
new_obj = deepcopy(self)
new_obj.__dict__.update(attributes)
new_obj.initialize()
return new_obj
