Plot API Example

In [1]:

# %pip install pycirclize

# %pip install pycirclize

1. Circos Class Plot¶

1-1. axis¶

In [2]:

from pycirclize import Circos

sectors = {"A": 10, "B": 20, "C": 15}
circos = Circos(sectors, space=5)
circos.axis()
fig = circos.plotfig()

from pycirclize import Circos sectors = {"A": 10, "B": 20, "C": 15} circos = Circos(sectors, space=5) circos.axis() fig = circos.plotfig()

In [3]:

from pycirclize import Circos

sectors = {"A": 10, "B": 20, "C": 15}
circos = Circos(sectors, end=270, space=5)
circos.axis(fc="lightgrey", ec="red")
fig = circos.plotfig()

from pycirclize import Circos sectors = {"A": 10, "B": 20, "C": 15} circos = Circos(sectors, end=270, space=5) circos.axis(fc="lightgrey", ec="red") fig = circos.plotfig()

1-2. text¶

In [4]:

from pycirclize import Circos
import math

sectors = {"A": 10, "B": 20, "C": 15}
circos = Circos(sectors, space=5)
circos.text("center")
circos.text("top", r=100)
circos.text("right", r=100, deg=90)
circos.text("right-middle", r=50, deg=90)
circos.text("bottom", r=100, deg=180)
circos.text("left", r=100, deg=270)
circos.text("left-top", r=100 * math.sqrt(2), deg=315)
fig = circos.plotfig()

from pycirclize import Circos import math sectors = {"A": 10, "B": 20, "C": 15} circos = Circos(sectors, space=5) circos.text("center") circos.text("top", r=100) circos.text("right", r=100, deg=90) circos.text("right-middle", r=50, deg=90) circos.text("bottom", r=100, deg=180) circos.text("left", r=100, deg=270) circos.text("left-top", r=100 * math.sqrt(2), deg=315) fig = circos.plotfig()

1-3. line¶

In [5]:

from pycirclize import Circos

sectors = {"A": 10, "B": 20, "C": 15}
circos = Circos(sectors, space=5)
circos.line(r=100)
circos.line(r=80, deg_lim=(0, 270), color="red")
circos.line(r=60, deg_lim=(90, 360), color="blue", lw=3, ls="dotted")
fig = circos.plotfig()

from pycirclize import Circos sectors = {"A": 10, "B": 20, "C": 15} circos = Circos(sectors, space=5) circos.line(r=100) circos.line(r=80, deg_lim=(0, 270), color="red") circos.line(r=60, deg_lim=(90, 360), color="blue", lw=3, ls="dotted") fig = circos.plotfig()

1-4. rect¶

In [6]:

from pycirclize import Circos

sectors = {"A": 10, "B": 20, "C": 15}
circos = Circos(sectors, space=5)
circos.rect(r_lim=(80, 100))
circos.rect(r_lim=(60, 80), deg_lim=(0, 270), fc="tomato")
circos.rect(r_lim=(30, 50), deg_lim=(90, 360), fc="lime", ec="grey", lw=2, hatch="//")
circos.rect(r_lim=(30, 100), deg_lim=(0, 90), fc="orange", alpha=0.2)
fig = circos.plotfig()

from pycirclize import Circos sectors = {"A": 10, "B": 20, "C": 15} circos = Circos(sectors, space=5) circos.rect(r_lim=(80, 100)) circos.rect(r_lim=(60, 80), deg_lim=(0, 270), fc="tomato") circos.rect(r_lim=(30, 50), deg_lim=(90, 360), fc="lime", ec="grey", lw=2, hatch="//") circos.rect(r_lim=(30, 100), deg_lim=(0, 90), fc="orange", alpha=0.2) fig = circos.plotfig()

1-5. link¶

In [7]:

from pycirclize import Circos

sectors = {"A": 10, "B": 20, "C": 15}
name2color = {"A": "red", "B": "blue", "C": "green"}
circos = Circos(sectors, space=5)
for sector in circos.sectors:
    track = sector.add_track((95, 100))
    track.axis(fc=name2color[sector.name])
    track.text(sector.name, color="white", size=12)
    track.xticks_by_interval(1)

# Plot links in various styles
circos.link(("A", 0, 1), ("A", 7, 8))
circos.link(("A", 1, 2), ("A", 7, 6), color="skyblue")
circos.link(("A", 9, 10), ("B", 4, 3), direction=1, color="tomato")
circos.link(("B", 5, 7), ("C", 6, 8), direction=1, ec="black", lw=1, hatch="//")
circos.link(("B", 18, 16), ("B", 11, 13), r1=90, r2=90, color="violet", ec="red", lw=2, ls="dashed")
circos.link(("C", 1, 3), ("B", 2, 0), direction=1, color="limegreen")
circos.link(("C", 11.5, 14), ("A", 4, 3), direction=2, color="chocolate", ec="black", lw=1, ls="dotted")

fig = circos.plotfig()

from pycirclize import Circos sectors = {"A": 10, "B": 20, "C": 15} name2color = {"A": "red", "B": "blue", "C": "green"} circos = Circos(sectors, space=5) for sector in circos.sectors: track = sector.add_track((95, 100)) track.axis(fc=name2color[sector.name]) track.text(sector.name, color="white", size=12) track.xticks_by_interval(1) # Plot links in various styles circos.link(("A", 0, 1), ("A", 7, 8)) circos.link(("A", 1, 2), ("A", 7, 6), color="skyblue") circos.link(("A", 9, 10), ("B", 4, 3), direction=1, color="tomato") circos.link(("B", 5, 7), ("C", 6, 8), direction=1, ec="black", lw=1, hatch="//") circos.link(("B", 18, 16), ("B", 11, 13), r1=90, r2=90, color="violet", ec="red", lw=2, ls="dashed") circos.link(("C", 1, 3), ("B", 2, 0), direction=1, color="limegreen") circos.link(("C", 11.5, 14), ("A", 4, 3), direction=2, color="chocolate", ec="black", lw=1, ls="dotted") fig = circos.plotfig()

1-6. link_line¶

In [8]:

from pycirclize import Circos

sectors = {"A": 10, "B": 20, "C": 15}
name2color = {"A": "red", "B": "blue", "C": "green"}
circos = Circos(sectors, space=5)
for sector in circos.sectors:
    track = sector.add_track((95, 100))
    track.axis(fc=name2color[sector.name])
    track.text(sector.name, color="white", size=12)
    track.xticks_by_interval(1)

# Plot link lines in various styles
circos.link_line(("A", 0), ("A", 7))
circos.link_line(("A", 9), ("B", 3), direction=1, color="red")
circos.link_line(("B", 5), ("B", 7), direction=-1, color="blue", lw=1.0)
circos.link_line(("B", 8), ("B", 15), r1=90, r2=90, direction=2, color="green", ls="dashed")

circos.link(("B", 17, 19), ("C", 11, 9), color="black")
circos.link_line(("B", 18), ("C", 10), direction=1, arrow_height=6, arrow_width=4, color="white", lw=1.0)

fig = circos.plotfig()

from pycirclize import Circos sectors = {"A": 10, "B": 20, "C": 15} name2color = {"A": "red", "B": "blue", "C": "green"} circos = Circos(sectors, space=5) for sector in circos.sectors: track = sector.add_track((95, 100)) track.axis(fc=name2color[sector.name]) track.text(sector.name, color="white", size=12) track.xticks_by_interval(1) # Plot link lines in various styles circos.link_line(("A", 0), ("A", 7)) circos.link_line(("A", 9), ("B", 3), direction=1, color="red") circos.link_line(("B", 5), ("B", 7), direction=-1, color="blue", lw=1.0) circos.link_line(("B", 8), ("B", 15), r1=90, r2=90, direction=2, color="green", ls="dashed") circos.link(("B", 17, 19), ("C", 11, 9), color="black") circos.link_line(("B", 18), ("C", 10), direction=1, arrow_height=6, arrow_width=4, color="white", lw=1.0) fig = circos.plotfig()

2. Sector Class Plot¶

2-1. axis¶

In [9]:

from pycirclize import Circos

sectors = {"A": 10, "B": 20, "C": 15}
circos = Circos(sectors, space=5)
sector_a = circos.get_sector("A")
sector_a.axis()
sector_b = circos.get_sector("B")
sector_b.axis(fc="lightgrey", lw=2, ls="dotted")
sector_c = circos.get_sector("C")
sector_c.axis(fc="tomato", ec="blue", hatch="//")
fig = circos.plotfig()

from pycirclize import Circos sectors = {"A": 10, "B": 20, "C": 15} circos = Circos(sectors, space=5) sector_a = circos.get_sector("A") sector_a.axis() sector_b = circos.get_sector("B") sector_b.axis(fc="lightgrey", lw=2, ls="dotted") sector_c = circos.get_sector("C") sector_c.axis(fc="tomato", ec="blue", hatch="//") fig = circos.plotfig()

2-2. text¶

In [10]:

from pycirclize import Circos

sectors = {"A": 10, "B": 20, "C": 15}
name2color = {"A": "red", "B": "blue", "C": "green"}
circos = Circos(sectors, space=5)
for sector in circos.sectors:
    sector.axis()
    sector.text(sector.name)
    sector.text(f"Center\n{sector.name}", r=50, size=12, color=name2color[sector.name])

fig = circos.plotfig()

from pycirclize import Circos sectors = {"A": 10, "B": 20, "C": 15} name2color = {"A": "red", "B": "blue", "C": "green"} circos = Circos(sectors, space=5) for sector in circos.sectors: sector.axis() sector.text(sector.name) sector.text(f"Center\n{sector.name}", r=50, size=12, color=name2color[sector.name]) fig = circos.plotfig()

2-3. line¶

In [11]:

from pycirclize import Circos

sectors = {"A": 10, "B": 20, "C": 15}
circos = Circos(sectors, space=5)
for sector in circos.sectors:
    sector.axis()
    sector.line(r=90)
    sector_center = (sector.start + sector.end) / 2
    sector.line(r=80, end=sector_center, color="red")
    sector.line(r=80, start=sector_center, color="blue")
    sector.line(r=60, color="green", lw=2, ls="dotted")

fig = circos.plotfig()

from pycirclize import Circos sectors = {"A": 10, "B": 20, "C": 15} circos = Circos(sectors, space=5) for sector in circos.sectors: sector.axis() sector.line(r=90) sector_center = (sector.start + sector.end) / 2 sector.line(r=80, end=sector_center, color="red") sector.line(r=80, start=sector_center, color="blue") sector.line(r=60, color="green", lw=2, ls="dotted") fig = circos.plotfig()

2-4. rect¶

In [12]:

from pycirclize import Circos
from pycirclize.utils import ColorCycler

ColorCycler.set_cmap("tab10")

sectors = {"A": 10, "B": 20, "C": 15}
circos = Circos(sectors, space=5)
for sector in circos.sectors:
    sector.axis()
    sector.rect(r_lim=(90, 100), fc="tomato")
    sector_center = (sector.start + sector.end) / 2
    sector.rect(end=sector_center, r_lim=(70, 80), color="skyblue")
    sector.rect(start=sector_center, r_lim=(70, 80), color="limegreen")
    for i in range(int(sector.size)):
        sector.rect(start=i, end=i + 1, r_lim=(50, 60), fc=ColorCycler(), ec="black", lw=1)
    sector.rect(sector.start + 3, sector.end - 3, r_lim=(30, 100), color="orange", alpha=0.2)

fig = circos.plotfig()

from pycirclize import Circos from pycirclize.utils import ColorCycler ColorCycler.set_cmap("tab10") sectors = {"A": 10, "B": 20, "C": 15} circos = Circos(sectors, space=5) for sector in circos.sectors: sector.axis() sector.rect(r_lim=(90, 100), fc="tomato") sector_center = (sector.start + sector.end) / 2 sector.rect(end=sector_center, r_lim=(70, 80), color="skyblue") sector.rect(start=sector_center, r_lim=(70, 80), color="limegreen") for i in range(int(sector.size)): sector.rect(start=i, end=i + 1, r_lim=(50, 60), fc=ColorCycler(), ec="black", lw=1) sector.rect(sector.start + 3, sector.end - 3, r_lim=(30, 100), color="orange", alpha=0.2) fig = circos.plotfig()

2-5. raster¶

In [13]:

from pycirclize import Circos
from pycirclize.utils import load_example_image_file

sectors = {"A": 10, "B": 15, "C": 12, "D": 20, "E": 15}
circos = Circos(sectors, space=5)
for sector in circos.sectors:
    # Plot line in sector region
    sector.axis(ec="grey")
    for r in range(10, 100, 10):
        sector.line(r=r, ec="lightgrey")
    # Plot raster image (python logo)
    logo_file = load_example_image_file("python_logo.png")
    sector.raster(logo_file, r=110, label=sector.name)
    sector.raster(logo_file, r=50, size=0.1, rotation="auto", border_width=5)
    sector.text(sector.name, r=62)

fig = circos.plotfig()

from pycirclize import Circos from pycirclize.utils import load_example_image_file sectors = {"A": 10, "B": 15, "C": 12, "D": 20, "E": 15} circos = Circos(sectors, space=5) for sector in circos.sectors: # Plot line in sector region sector.axis(ec="grey") for r in range(10, 100, 10): sector.line(r=r, ec="lightgrey") # Plot raster image (python logo) logo_file = load_example_image_file("python_logo.png") sector.raster(logo_file, r=110, label=sector.name) sector.raster(logo_file, r=50, size=0.1, rotation="auto", border_width=5) sector.text(sector.name, r=62) fig = circos.plotfig()

3. Track Class Plot¶

3-1. axis¶

In [14]:

from pycirclize import Circos

sectors = {"A": 10, "B": 20, "C": 15}
circos = Circos(sectors, space=5)
for sector in circos.sectors:
    track1 = sector.add_track((90, 100))
    track1.axis()
    track2 = sector.add_track((70, 80))
    track2.axis(fc="lightgrey")

fig = circos.plotfig()

from pycirclize import Circos sectors = {"A": 10, "B": 20, "C": 15} circos = Circos(sectors, space=5) for sector in circos.sectors: track1 = sector.add_track((90, 100)) track1.axis() track2 = sector.add_track((70, 80)) track2.axis(fc="lightgrey") fig = circos.plotfig()

3-2. text¶

In [15]:

from pycirclize import Circos

sectors = {"A": 10, "B": 20, "C": 15}
circos = Circos(sectors, space=5)
for sector in circos.sectors:
    track1 = sector.add_track((90, 100))
    track1.axis()
    track1.text(sector.name)
    track2 = sector.add_track((70, 80))
    track2.axis(fc="lightgrey")
    track2.text(sector.name, orientation="vertical", color="red", size=15)

fig = circos.plotfig()

from pycirclize import Circos sectors = {"A": 10, "B": 20, "C": 15} circos = Circos(sectors, space=5) for sector in circos.sectors: track1 = sector.add_track((90, 100)) track1.axis() track1.text(sector.name) track2 = sector.add_track((70, 80)) track2.axis(fc="lightgrey") track2.text(sector.name, orientation="vertical", color="red", size=15) fig = circos.plotfig()

3-3. rect¶

In [16]:

from pycirclize import Circos
from pycirclize.utils import ColorCycler
ColorCycler.set_cmap("tab10")

sectors = {"A": 10, "B": 20, "C": 15}
circos = Circos(sectors, space=5)
for sector in circos.sectors:
    track1 = sector.add_track((90, 100))
    track1.axis()
    # Plot rect & text (style1)
    for i in range(int(track1.size)):
        start, end = i, i + 1
        track1.rect(start, end, fc=ColorCycler())
        track1.text(str(end), (end + start) / 2)
    # Plot rect & text (style2)
    track2 = sector.add_track((70, 80))
    for i in range(int(track2.size)):
        start, end = i, i + 1
        track2.rect(start, end, fc=ColorCycler(), ec="white", lw=1)
        track2.text(str(end), (end + start) / 2, color="white", orientation="vertical")

fig = circos.plotfig()

from pycirclize import Circos from pycirclize.utils import ColorCycler ColorCycler.set_cmap("tab10") sectors = {"A": 10, "B": 20, "C": 15} circos = Circos(sectors, space=5) for sector in circos.sectors: track1 = sector.add_track((90, 100)) track1.axis() # Plot rect & text (style1) for i in range(int(track1.size)): start, end = i, i + 1 track1.rect(start, end, fc=ColorCycler()) track1.text(str(end), (end + start) / 2) # Plot rect & text (style2) track2 = sector.add_track((70, 80)) for i in range(int(track2.size)): start, end = i, i + 1 track2.rect(start, end, fc=ColorCycler(), ec="white", lw=1) track2.text(str(end), (end + start) / 2, color="white", orientation="vertical") fig = circos.plotfig()

3-4. arrow¶

In [17]:

from pycirclize import Circos
from pycirclize.utils import ColorCycler

ColorCycler.set_cmap("tab10")

sectors = {"A": 10, "B": 20, "C": 15}
circos = Circos(sectors, space=5)
for sector in circos.sectors:
    sector.axis()
    # Plot forward arrow with default style
    track1 = sector.add_track((90, 100))
    for i in range(int(track1.size)):
        start, end = i, i + 1
        track1.arrow(start, end, fc=ColorCycler())
    # Plot reverse arrow with user-specified style
    track2 = sector.add_track((70, 80))
    for i in range(int(track2.size)):
        start, end = i, i + 1
        track2.arrow(end, start, head_length=4, shaft_ratio=1.0, fc=ColorCycler(), ec="black", lw=0.5)

fig = circos.plotfig()

from pycirclize import Circos from pycirclize.utils import ColorCycler ColorCycler.set_cmap("tab10") sectors = {"A": 10, "B": 20, "C": 15} circos = Circos(sectors, space=5) for sector in circos.sectors: sector.axis() # Plot forward arrow with default style track1 = sector.add_track((90, 100)) for i in range(int(track1.size)): start, end = i, i + 1 track1.arrow(start, end, fc=ColorCycler()) # Plot reverse arrow with user-specified style track2 = sector.add_track((70, 80)) for i in range(int(track2.size)): start, end = i, i + 1 track2.arrow(end, start, head_length=4, shaft_ratio=1.0, fc=ColorCycler(), ec="black", lw=0.5) fig = circos.plotfig()

3-5. xticks¶

In [18]:

from pycirclize import Circos

sectors = {"A": 10, "B": 20, "C": 15}
circos = Circos(sectors, space=5)
for sector in circos.sectors:
    track1 = sector.add_track((90, 100))
    track1.axis()
    # Plot outer xticks
    pos_list = list(range(0, int(track1.size) + 1))
    labels = [f"{i:02d}" for i in pos_list]
    track1.xticks(pos_list, labels)
    # Plot inner xticks label
    labels = [f"Label{i:02d}" for i in pos_list]
    track1.xticks(
        pos_list,
        labels,
        outer=False,
        tick_length=0,
        label_margin=2,
        label_orientation="vertical",
    )
fig = circos.plotfig()

from pycirclize import Circos sectors = {"A": 10, "B": 20, "C": 15} circos = Circos(sectors, space=5) for sector in circos.sectors: track1 = sector.add_track((90, 100)) track1.axis() # Plot outer xticks pos_list = list(range(0, int(track1.size) + 1)) labels = [f"{i:02d}" for i in pos_list] track1.xticks(pos_list, labels) # Plot inner xticks label labels = [f"Label{i:02d}" for i in pos_list] track1.xticks( pos_list, labels, outer=False, tick_length=0, label_margin=2, label_orientation="vertical", ) fig = circos.plotfig()

3-6. xticks_by_interval¶

3-6-1. Small interval¶

In [19]:

from pycirclize import Circos

sectors = {"A": 10, "B": 20, "C": 15}
circos = Circos(sectors, space=5)
for sector in circos.sectors:
    # Plot outer xticks
    track1 = sector.add_track((90, 100))
    track1.axis()
    track1.xticks_by_interval(1, label_size=12)
    # Plot inner xticks
    track2 = sector.add_track((70, 80))
    track2.xticks_by_interval(
        2,
        outer=False,
        show_bottom_line=True,
        label_orientation="vertical",
        line_kws=dict(color="red"),
        text_kws=dict(color="blue"),
    )
fig = circos.plotfig()

from pycirclize import Circos sectors = {"A": 10, "B": 20, "C": 15} circos = Circos(sectors, space=5) for sector in circos.sectors: # Plot outer xticks track1 = sector.add_track((90, 100)) track1.axis() track1.xticks_by_interval(1, label_size=12) # Plot inner xticks track2 = sector.add_track((70, 80)) track2.xticks_by_interval( 2, outer=False, show_bottom_line=True, label_orientation="vertical", line_kws=dict(color="red"), text_kws=dict(color="blue"), ) fig = circos.plotfig()

3-6-2. Large interval¶

In [20]:

from pycirclize import Circos

sectors = {"A": 10000000, "B": 20000000, "C": 15000000}
circos = Circos(sectors, space=5)
for sector in circos.sectors:
    # Major & Minor xticks
    track1 = sector.add_track((90, 100))
    track1.axis()
    mb_size = 1000000
    track1.xticks_by_interval(mb_size, label_orientation="vertical")
    track1.xticks_by_interval(mb_size / 5, tick_length=1, show_label=False)
    # Mb formatted xticks
    track2 = sector.add_track((80, 90))
    track2.xticks_by_interval(
        mb_size,
        outer=False,
        show_bottom_line=True,
        label_orientation="vertical",
        label_formatter=lambda v: f"{v / mb_size:.1f} Mb",
    )
fig = circos.plotfig()

from pycirclize import Circos sectors = {"A": 10000000, "B": 20000000, "C": 15000000} circos = Circos(sectors, space=5) for sector in circos.sectors: # Major & Minor xticks track1 = sector.add_track((90, 100)) track1.axis() mb_size = 1000000 track1.xticks_by_interval(mb_size, label_orientation="vertical") track1.xticks_by_interval(mb_size / 5, tick_length=1, show_label=False) # Mb formatted xticks track2 = sector.add_track((80, 90)) track2.xticks_by_interval( mb_size, outer=False, show_bottom_line=True, label_orientation="vertical", label_formatter=lambda v: f"{v / mb_size:.1f} Mb", ) fig = circos.plotfig()

3-7. yticks¶

In [21]:

from pycirclize import Circos

sectors = {"A": 10000000, "B": 20000000, "C": 15000000}
circos = Circos(sectors, space=15)
for sector in circos.sectors:
    # Plot yticks
    track1 = sector.add_track((80, 100))
    track1.axis()
    y = [0, 5, 10, 15, 20]
    y_labels = list(map(str, y))
    track1.yticks(y, y_labels)
    # Plot yticks label on left side
    track2 = sector.add_track((50, 70), r_pad_ratio=0.1)
    track2.axis()
    y = [10, 15, 20]
    y_labels = ["Label1", "Label2", "Label3"]
    track2.yticks(y, y_labels, vmin=10, vmax=25, side="left", line_kws=dict(color="red", lw=1), text_kws=dict(color="blue"))

fig = circos.plotfig()

from pycirclize import Circos sectors = {"A": 10000000, "B": 20000000, "C": 15000000} circos = Circos(sectors, space=15) for sector in circos.sectors: # Plot yticks track1 = sector.add_track((80, 100)) track1.axis() y = [0, 5, 10, 15, 20] y_labels = list(map(str, y)) track1.yticks(y, y_labels) # Plot yticks label on left side track2 = sector.add_track((50, 70), r_pad_ratio=0.1) track2.axis() y = [10, 15, 20] y_labels = ["Label1", "Label2", "Label3"] track2.yticks(y, y_labels, vmin=10, vmax=25, side="left", line_kws=dict(color="red", lw=1), text_kws=dict(color="blue")) fig = circos.plotfig()

3-8. grid¶

In [22]:

from pycirclize import Circos
import numpy as np
np.random.seed(0)

sectors = {"A": 10, "B": 20, "C": 15}
circos = Circos(sectors, space=5)
for sector in circos.sectors:
    # Plot Y-axis grid line (Default: 6 grid line)
    track1 = sector.add_track((80, 100), r_pad_ratio=0.1)
    track1.axis()
    track1.xticks_by_interval(interval=1)
    track1.grid()
    # Plot X-axis grid line (interval=1)
    track2 = sector.add_track((55, 75))
    track2.axis()
    track2.grid(y_grid_num=None, x_grid_interval=1, color="red")
    # Plot both XY-axis grid line
    track3 = sector.add_track((30, 50))
    track3.grid(y_grid_num=11, x_grid_interval=0.5, color="blue", ls="dashed")

fig = circos.plotfig()

from pycirclize import Circos import numpy as np np.random.seed(0) sectors = {"A": 10, "B": 20, "C": 15} circos = Circos(sectors, space=5) for sector in circos.sectors: # Plot Y-axis grid line (Default: 6 grid line) track1 = sector.add_track((80, 100), r_pad_ratio=0.1) track1.axis() track1.xticks_by_interval(interval=1) track1.grid() # Plot X-axis grid line (interval=1) track2 = sector.add_track((55, 75)) track2.axis() track2.grid(y_grid_num=None, x_grid_interval=1, color="red") # Plot both XY-axis grid line track3 = sector.add_track((30, 50)) track3.grid(y_grid_num=11, x_grid_interval=0.5, color="blue", ls="dashed") fig = circos.plotfig()

3-9. line¶

In [23]:

from pycirclize import Circos
import numpy as np
np.random.seed(0)

sectors = {"A": 10, "B": 20, "C": 15}
circos = Circos(sectors, space=5)
for sector in circos.sectors:
    track = sector.add_track((80, 100), r_pad_ratio=0.1)
    track.axis()
    track.xticks_by_interval(1)
    vmin, vmax = 0, 10
    # Line between start-end two points
    track.line([track.start, track.end], [vmin, vmax], lw=1.5, ls="dotted")
    # Line of random value points
    x = np.linspace(track.start, track.end, int(track.size) * 5 + 1)
    y = np.random.randint(vmin, vmax, len(x))
    track.line(x, y)
fig = circos.plotfig()

from pycirclize import Circos import numpy as np np.random.seed(0) sectors = {"A": 10, "B": 20, "C": 15} circos = Circos(sectors, space=5) for sector in circos.sectors: track = sector.add_track((80, 100), r_pad_ratio=0.1) track.axis() track.xticks_by_interval(1) vmin, vmax = 0, 10 # Line between start-end two points track.line([track.start, track.end], [vmin, vmax], lw=1.5, ls="dotted") # Line of random value points x = np.linspace(track.start, track.end, int(track.size) * 5 + 1) y = np.random.randint(vmin, vmax, len(x)) track.line(x, y) fig = circos.plotfig()

3-10. scatter¶

In [24]:

from pycirclize import Circos
import numpy as np
np.random.seed(0)

sectors = {"A": 10, "B": 20, "C": 15}
circos = Circos(sectors, space=5)
for sector in circos.sectors:
    track = sector.add_track((80, 100), r_pad_ratio=0.1)
    track.axis()
    track.xticks_by_interval(1)
    vmin, vmax = 0, 10
    x = np.linspace(track.start, track.end, int(track.size) * 5 + 1)
    y = np.random.randint(vmin, vmax, len(x))
    track.scatter(x, y)
fig = circos.plotfig()

from pycirclize import Circos import numpy as np np.random.seed(0) sectors = {"A": 10, "B": 20, "C": 15} circos = Circos(sectors, space=5) for sector in circos.sectors: track = sector.add_track((80, 100), r_pad_ratio=0.1) track.axis() track.xticks_by_interval(1) vmin, vmax = 0, 10 x = np.linspace(track.start, track.end, int(track.size) * 5 + 1) y = np.random.randint(vmin, vmax, len(x)) track.scatter(x, y) fig = circos.plotfig()

3-11. bar¶

In [25]:

from pycirclize import Circos
from pycirclize.utils import ColorCycler
import numpy as np
np.random.seed(0)

sectors = {"A": 10, "B": 20, "C": 15}
circos = Circos(sectors, space=5)
for sector in circos.sectors:
    vmin, vmax = 1, 10
    x = np.linspace(sector.start + 0.5, sector.end - 0.5, int(sector.size))
    y = np.random.randint(vmin, vmax, len(x))
    # Plot bar (default)
    track1 = sector.add_track((80, 100), r_pad_ratio=0.1)
    track1.axis()
    track1.xticks_by_interval(1)
    track1.xticks_by_interval(0.1, tick_length=1, show_label=False)
    track1.bar(x, y)
    # Plot stacked bar with user-specified params
    track2 = sector.add_track((50, 70))
    track2.axis()
    track2.xticks_by_interval(1, outer=False)

    ColorCycler.set_cmap("tab10")
    tab10_colors = [ColorCycler() for _ in range(len(x))]
    track2.bar(x, y, width=1.0, color=tab10_colors, ec="grey", lw=0.5, vmax=vmax * 2)

    ColorCycler.set_cmap("Pastel1")
    pastel_colors = [ColorCycler() for _ in range(len(x))]
    y2 = np.random.randint(vmin, vmax, len(x))
    track2.bar(x, y2, width=1.0, bottom=y, color=pastel_colors, ec="grey", lw=0.5, hatch="//", vmax=vmax * 2)

fig = circos.plotfig()

from pycirclize import Circos from pycirclize.utils import ColorCycler import numpy as np np.random.seed(0) sectors = {"A": 10, "B": 20, "C": 15} circos = Circos(sectors, space=5) for sector in circos.sectors: vmin, vmax = 1, 10 x = np.linspace(sector.start + 0.5, sector.end - 0.5, int(sector.size)) y = np.random.randint(vmin, vmax, len(x)) # Plot bar (default) track1 = sector.add_track((80, 100), r_pad_ratio=0.1) track1.axis() track1.xticks_by_interval(1) track1.xticks_by_interval(0.1, tick_length=1, show_label=False) track1.bar(x, y) # Plot stacked bar with user-specified params track2 = sector.add_track((50, 70)) track2.axis() track2.xticks_by_interval(1, outer=False) ColorCycler.set_cmap("tab10") tab10_colors = [ColorCycler() for _ in range(len(x))] track2.bar(x, y, width=1.0, color=tab10_colors, ec="grey", lw=0.5, vmax=vmax * 2) ColorCycler.set_cmap("Pastel1") pastel_colors = [ColorCycler() for _ in range(len(x))] y2 = np.random.randint(vmin, vmax, len(x)) track2.bar(x, y2, width=1.0, bottom=y, color=pastel_colors, ec="grey", lw=0.5, hatch="//", vmax=vmax * 2) fig = circos.plotfig()

3-12. fill_between¶

In [26]:

from pycirclize import Circos
import numpy as np
np.random.seed(0)

sectors = {"A": 10, "B": 20, "C": 15}
circos = Circos(sectors, space=5)
for sector in circos.sectors:
    vmin, vmax = 0, 10
    # Plot fill_between with simple lines
    track1 = sector.add_track((80, 100), r_pad_ratio=0.1)
    track1.axis()
    track1.xticks_by_interval(1)
    track1.fill_between(x=[track1.start, track1.end], y1=[vmin, vmax], y2=[vmin, vmax / 2])
    # Plot fill_between with random points line
    track2 = sector.add_track((50, 70), r_pad_ratio=0.1)
    track2.axis()
    x = np.linspace(track2.start, track2.end, int(track2.size) * 5 + 1)
    y = np.random.randint(vmin, vmax, len(x))
    track2.fill_between(x, y, ec="black", lw=1, ls="dashed")

fig = circos.plotfig()

from pycirclize import Circos import numpy as np np.random.seed(0) sectors = {"A": 10, "B": 20, "C": 15} circos = Circos(sectors, space=5) for sector in circos.sectors: vmin, vmax = 0, 10 # Plot fill_between with simple lines track1 = sector.add_track((80, 100), r_pad_ratio=0.1) track1.axis() track1.xticks_by_interval(1) track1.fill_between(x=[track1.start, track1.end], y1=[vmin, vmax], y2=[vmin, vmax / 2]) # Plot fill_between with random points line track2 = sector.add_track((50, 70), r_pad_ratio=0.1) track2.axis() x = np.linspace(track2.start, track2.end, int(track2.size) * 5 + 1) y = np.random.randint(vmin, vmax, len(x)) track2.fill_between(x, y, ec="black", lw=1, ls="dashed") fig = circos.plotfig()

3-13. heatmap¶

In [27]:

from pycirclize import Circos
import numpy as np
np.random.seed(0)

sectors = {"A": 10, "B": 20, "C": 15}
circos = Circos(sectors, space=10)
vmin1, vmax1 = 0, 10
vmin2, vmax2 = -100, 100
for sector in circos.sectors:
    # Plot heatmap
    track1 = sector.add_track((80, 100))
    track1.axis()
    track1.xticks_by_interval(1)
    data = np.random.randint(vmin1, vmax1 + 1, (4, int(sector.size)))
    track1.heatmap(data, vmin=vmin1, vmax=vmax1, show_value=True)
    # Plot heatmap with labels
    track2 = sector.add_track((50, 70))
    track2.axis()
    x = np.linspace(1, int(track2.size), int(track2.size)) - 0.5
    xlabels = [str(int(v + 1)) for v in x]
    track2.xticks(x, xlabels, outer=False)
    track2.yticks([0.5, 1.5, 2.5, 3.5, 4.5], list("ABCDE"), vmin=0, vmax=5)
    data = np.random.randint(vmin2, vmax2 + 1, (5, int(sector.size)))
    track2.heatmap(data, vmin=vmin2, vmax=vmax2, cmap="viridis", rect_kws=dict(ec="white", lw=1))

circos.colorbar(bounds=(0.35, 0.55, 0.3, 0.01), vmin=vmin1, vmax=vmax1, orientation="horizontal")
circos.colorbar(bounds=(0.35, 0.45, 0.3, 0.01), vmin=vmin2, vmax=vmax2, orientation="horizontal", cmap="viridis")

fig = circos.plotfig()

from pycirclize import Circos import numpy as np np.random.seed(0) sectors = {"A": 10, "B": 20, "C": 15} circos = Circos(sectors, space=10) vmin1, vmax1 = 0, 10 vmin2, vmax2 = -100, 100 for sector in circos.sectors: # Plot heatmap track1 = sector.add_track((80, 100)) track1.axis() track1.xticks_by_interval(1) data = np.random.randint(vmin1, vmax1 + 1, (4, int(sector.size))) track1.heatmap(data, vmin=vmin1, vmax=vmax1, show_value=True) # Plot heatmap with labels track2 = sector.add_track((50, 70)) track2.axis() x = np.linspace(1, int(track2.size), int(track2.size)) - 0.5 xlabels = [str(int(v + 1)) for v in x] track2.xticks(x, xlabels, outer=False) track2.yticks([0.5, 1.5, 2.5, 3.5, 4.5], list("ABCDE"), vmin=0, vmax=5) data = np.random.randint(vmin2, vmax2 + 1, (5, int(sector.size))) track2.heatmap(data, vmin=vmin2, vmax=vmax2, cmap="viridis", rect_kws=dict(ec="white", lw=1)) circos.colorbar(bounds=(0.35, 0.55, 0.3, 0.01), vmin=vmin1, vmax=vmax1, orientation="horizontal") circos.colorbar(bounds=(0.35, 0.45, 0.3, 0.01), vmin=vmin2, vmax=vmax2, orientation="horizontal", cmap="viridis") fig = circos.plotfig()

3-14. tree¶

In [28]:

from pycirclize import Circos
from pycirclize.utils import load_example_tree_file
from Bio import Phylo

# Load newick tree
tree_file = load_example_tree_file("alphabet.nwk")
tree = Phylo.read(tree_file, "newick")
# Initialize circos sector by tree size
circos = Circos(sectors=dict(tree=tree.count_terminals()))
sector = circos.sectors[0]
# Plot tree
track = sector.add_track((50, 100))
track.tree(tree)

fig = circos.plotfig()

from pycirclize import Circos from pycirclize.utils import load_example_tree_file from Bio import Phylo # Load newick tree tree_file = load_example_tree_file("alphabet.nwk") tree = Phylo.read(tree_file, "newick") # Initialize circos sector by tree size circos = Circos(sectors=dict(tree=tree.count_terminals())) sector = circos.sectors[0] # Plot tree track = sector.add_track((50, 100)) track.tree(tree) fig = circos.plotfig()

3-15. genomic_features¶

3-15-1. Genbank file¶

In [29]:

from pycirclize import Circos
from pycirclize.utils import load_prokaryote_example_file
from pycirclize.parser import Genbank

# Load Genbank file
gbk_file = load_prokaryote_example_file("enterobacteria_phage.gbk")
gbk = Genbank(gbk_file)
# Initialize circos instance
seqid2size = gbk.get_seqid2size()
space = 0 if len(seqid2size) == 1 else 2
circos = Circos(sectors=seqid2size, space=space)
circos.text("Enterobacteria phage\n(NC_000902)", size=15)

seqid2features = gbk.get_seqid2features("CDS")
for sector in circos.sectors:
    # Setup outer track
    outer_track = sector.add_track((99.7, 100))
    outer_track.axis(fc="black")
    outer_track.xticks_by_interval(5000, label_formatter=lambda v: f"{v / 1000:.0f} Kb")
    outer_track.xticks_by_interval(1000, tick_length=1, show_label=False)
    # Plot forward & reverse CDS genomic features
    cds_track = sector.add_track((93, 98))
    for feature in seqid2features[sector.name]:
        color = "salmon" if feature.location.strand == 1 else "skyblue"
        cds_track.genomic_features(feature, plotstyle="arrow", fc=color)

fig = circos.plotfig()

from pycirclize import Circos from pycirclize.utils import load_prokaryote_example_file from pycirclize.parser import Genbank # Load Genbank file gbk_file = load_prokaryote_example_file("enterobacteria_phage.gbk") gbk = Genbank(gbk_file) # Initialize circos instance seqid2size = gbk.get_seqid2size() space = 0 if len(seqid2size) == 1 else 2 circos = Circos(sectors=seqid2size, space=space) circos.text("Enterobacteria phage\n(NC_000902)", size=15) seqid2features = gbk.get_seqid2features("CDS") for sector in circos.sectors: # Setup outer track outer_track = sector.add_track((99.7, 100)) outer_track.axis(fc="black") outer_track.xticks_by_interval(5000, label_formatter=lambda v: f"{v / 1000:.0f} Kb") outer_track.xticks_by_interval(1000, tick_length=1, show_label=False) # Plot forward & reverse CDS genomic features cds_track = sector.add_track((93, 98)) for feature in seqid2features[sector.name]: color = "salmon" if feature.location.strand == 1 else "skyblue" cds_track.genomic_features(feature, plotstyle="arrow", fc=color) fig = circos.plotfig()

3-15-2. GFF file¶

In [30]:

from pycirclize import Circos
from pycirclize.utils import load_prokaryote_example_file, ColorCycler
from pycirclize.parser import Gff
ColorCycler.set_cmap("Set3")

# Load GFF file
gff_file = load_prokaryote_example_file("escherichia_coli.gff.gz")
gff = Gff(gff_file)
# Initialize circos instance
seqid2size= gff.get_seqid2size()
space = 0 if len(seqid2size) == 1 else 2
circos = Circos(sectors=seqid2size, space=space)
circos.text("Escherichia coli\n(NC_000913)", size=15)

seqid2features = gff.get_seqid2features(feature_type=None)
for sector in circos.sectors:
    # Setup outer track
    outer_track = sector.add_track((98, 100))
    outer_track.axis(fc="lightgrey")
    outer_track.xticks_by_interval(500000, label_formatter=lambda v: f"{v / 1000000:.1f} Mb")
    outer_track.xticks_by_interval(100000, tick_length=1, show_label=False)
    # Plot forward/reverse CDS, rRNA, tRNA tracks
    f_cds_track = sector.add_track((88, 95), r_pad_ratio=0.1)
    r_cds_track = sector.add_track((81, 88), r_pad_ratio=0.1)
    rrna_track = sector.add_track((74, 81), r_pad_ratio=0.1)
    trna_track = sector.add_track((67, 74), r_pad_ratio=0.1)
    for feature in seqid2features[sector.name]:
        if feature.type == "CDS":
            if feature.location.strand == 1:
                f_cds_track.genomic_features(feature, fc=ColorCycler())
            else:
                r_cds_track.genomic_features(feature, fc=ColorCycler())
        elif feature.type == "rRNA":
            rrna_track.genomic_features(feature, fc="limegreen")
        elif feature.type == "tRNA":
            trna_track.genomic_features(feature, color="magenta", lw=0.1)  # Set lw=0.1 to enphasize small tRNA plot

fig = circos.plotfig()

from pycirclize import Circos from pycirclize.utils import load_prokaryote_example_file, ColorCycler from pycirclize.parser import Gff ColorCycler.set_cmap("Set3") # Load GFF file gff_file = load_prokaryote_example_file("escherichia_coli.gff.gz") gff = Gff(gff_file) # Initialize circos instance seqid2size= gff.get_seqid2size() space = 0 if len(seqid2size) == 1 else 2 circos = Circos(sectors=seqid2size, space=space) circos.text("Escherichia coli\n(NC_000913)", size=15) seqid2features = gff.get_seqid2features(feature_type=None) for sector in circos.sectors: # Setup outer track outer_track = sector.add_track((98, 100)) outer_track.axis(fc="lightgrey") outer_track.xticks_by_interval(500000, label_formatter=lambda v: f"{v / 1000000:.1f} Mb") outer_track.xticks_by_interval(100000, tick_length=1, show_label=False) # Plot forward/reverse CDS, rRNA, tRNA tracks f_cds_track = sector.add_track((88, 95), r_pad_ratio=0.1) r_cds_track = sector.add_track((81, 88), r_pad_ratio=0.1) rrna_track = sector.add_track((74, 81), r_pad_ratio=0.1) trna_track = sector.add_track((67, 74), r_pad_ratio=0.1) for feature in seqid2features[sector.name]: if feature.type == "CDS": if feature.location.strand == 1: f_cds_track.genomic_features(feature, fc=ColorCycler()) else: r_cds_track.genomic_features(feature, fc=ColorCycler()) elif feature.type == "rRNA": rrna_track.genomic_features(feature, fc="limegreen") elif feature.type == "tRNA": trna_track.genomic_features(feature, color="magenta", lw=0.1) # Set lw=0.1 to enphasize small tRNA plot fig = circos.plotfig()