Colormaps of Hi-C contact map¶

[1]:

import coolbox
from coolbox.api import *

[2]:

coolbox.__version__

[2]:

'0.3.0'

[3]:

cool_path = "../../../tests/test_data/cool_chr9_4000000_6000000.mcool"
test_region = "chr9:4300000-5700000"

Matplotlib builtin colormaps¶

Full colormap list can reference this page.

[4]:

with Feature(depth_ratio=0.4):
    frame = XAxis() + \
        Cool(cool_path, cmap="YlOrRd") + \
        Cool(cool_path, cmap="Blues") + \
        Cool(cool_path, cmap="RdPu") + \
        Cool(cool_path, cmap="RdYlBu_r")

frame.plot(test_region)

[4]:

../_images/_gallery_hicmat_cmaps_5_0.png

Color maps defined in coolbox¶

[5]:

from coolbox.core.track.hicmat.plot import cmaps

[6]:

cmaps

[6]:

{'JuiceBoxLike': <matplotlib.colors.LinearSegmentedColormap at 0x7f921a082cd0>,
 'JuiceBoxLike2': <matplotlib.colors.LinearSegmentedColormap at 0x7f921a082ca0>}

[7]:

frame = XAxis() + \
    Cool(cool_path, cmap="JuiceBoxLike")

frame.plot("chr9:4000000-6000000")

[7]:

../_images/_gallery_hicmat_cmaps_9_0.png

Define new colormap with matplotlib¶

Here, give an example of create cmap using LinearSegementedColormap:

[8]:

from matplotlib.colors import LinearSegmentedColormap

# give a list of color (color gradient)
gradient = ['#FFFFFF','#FFDFAF','#FF7555','#FF2600','#F70000']

my_cmap = LinearSegmentedColormap.from_list('interaction', gradient)
my_cmap.set_bad("white")
my_cmap.set_under("white")

[9]:

frame = XAxis() + \
    Cool(cool_path, cmap=my_cmap)

frame.plot("chr9:4000000-6000000")

[9]:

../_images/_gallery_hicmat_cmaps_13_0.png