Arcs style

[1]:

import sys; sys.path.insert(0, "../../../")
import coolbox
from coolbox.api import *

[2]:

coolbox.__version__

[2]:

'0.4.0'

[3]:

bedpe_path = "../../../tests/test_data/bedpe_var_chr9_4000000_6000000.bedpe"

Open region

The “open_region” parameter control the behavior of contact fetching. If specified to False, will only fetch the contacts which it’s double sides located in the region.

[4]:

arc = Arcs(bedpe_path, open_region=False) + TrackHeight(5)
frame = XAxis() + arc

frame.plot("chr9:4500000-6000000")

realloc(): invalid next size

[4]:

Otherwise(default), will fetch the contacts only one side located in the region:

[5]:

arc = Arcs(bedpe_path, open_region=True) + TrackHeight(5)
frame = XAxis() + arc

frame.plot("chr9:4500000-6000000")

[5]:

Line width

Arcs will calculate the line width according to the contacts score specifed in BEDPE file. When you use Pairs file or scores are not provided in BEDPE, score will set to 1.

The default width calculation equation is: 0.5 + math.sqrt(score) You can change it with score_to_width parameter:

[6]:

arc = Arcs(bedpe_path, score_to_width="0.5 + np.log(score)") + TrackHeight(5)
frame = XAxis() + arc

frame.plot("chr9:4500000-6000000")

[6]:

If the static line width is needed, use the line_width parameter:

[7]:

arc = Arcs(bedpe_path, line_width=2) + TrackHeight(5)
frame = XAxis() + arc

frame.plot("chr9:4500000-6000000")

[7]:

Fill

Set the fill=True to fill arc area, and adjust color and alpha with fill_color, fill_alpha parameters:

[8]:

arc = Arcs(bedpe_path, fill=True, fill_alpha=0.2, fill_color="#3297dc") + TrackHeight(8)
frame = XAxis() + arc

frame.plot("chr9:4500000-6000000")

[8]:

Height

The arc height is calculate from it’s diameter(xmax - xmin), the default equation is: (max_height - 0.5) * diameter / max_diameter. It can be changed with diameter_to_height parameter, for example to use static height:

[9]:

arc = Arcs(bedpe_path, diameter_to_height="max_height-0.5") + TrackHeight(8)
frame = XAxis() + arc

frame.plot("chr9:4500000-6000000")

[9]:

Let shorter arcs has higher than longer:

[10]:

arc = Arcs(bedpe_path, diameter_to_height="(max_diameter/diameter)*0.5") + TrackHeight(8)
frame = XAxis() + arc

frame.plot("chr9:4500000-6000000")

[10]:

Line style

see linestyles.

[11]:

arc = Arcs(bedpe_path, line_style="dotted") + TrackHeight(8)
frame = XAxis() + arc

frame.plot("chr9:4500000-6000000")

[11]:

Color

Arcs deafault use statical color, set with color parameter:

[12]:

arc = Arcs(bedpe_path, color="red") + TrackHeight(8)
frame = XAxis() + arc

frame.plot("chr9:4500000-6000000")

[12]:

Dynamic color can be enabled with “cmap”, here is a example, other ColorMap can reference here.

[13]:

arc = Arcs(bedpe_path, cmap="Reds", vmin=0, vmax=30) + TrackHeight(8)
frame = XAxis() + arc

frame.plot("chr9:4500000-6000000")

[13]:

Orientation

Arcs canbe inverted:

[14]:

arc = Arcs(bedpe_path) + Inverted() + TrackHeight(8)
# Or:
#arc = Arcs(bedpe_path, orientation="inverted") + TrackHeight(8)
frame = XAxis() + arc

frame.plot("chr9:4500000-6000000")

[14]: