Plot Tips

In [1]:

# %pip install pycirclizely

# %pip install pycirclizely

In [2]:

import plotly.io as pio
from IPython.display import HTML

import plotly.io as pio from IPython.display import HTML

Grouping Sectors¶

In pyCirclizely, the space size between sectors can be set arbitrarily. By using the calc_group_spaces function, users can easily get the sector space size setting within/between groups based on the number of groups. Groups can be explicitly visualized as shown in the code example below.

In [3]:

from pycirclizely import Circos
from pycirclizely.utils import ColorCycler, calc_group_spaces

sectors = {name: 10 for name in "ABCDEFGHIJ"}
group1, group2, group3 = list("ABCD"), list("EFG"), list("HIJ")

# Calculate appropriate group between/within spaces
# In this example, 10 sectors are displayed as groups dividied into [4, 3, 3]
spaces = calc_group_spaces([4, 3, 3], space_bw_group=15, space_in_group=2)
circos = Circos(sectors, space=spaces)

# Plot sector track
color_cycler = ColorCycler("Set3")
for sector in circos.sectors:
    track = sector.add_track(r_lim=(85, 90))
    track.axis(fillcolor=color_cycler.get_color())
    track.text(sector.name)

# Plot group sectors range
color_cycler = ColorCycler("T10")
for idx, group in enumerate((group1, group2, group3), 1):
    group_deg_lim = circos.get_group_sectors_deg_lim(group)
    circos.rect(
        r_lim=(97, 100),
        deg_lim=group_deg_lim,
        fillcolor=color_cycler.get_color(),
        line=dict(color="black", width=0.5),
    )
    group_center_deg = sum(group_deg_lim) / 2
    circos.text(f"Group{idx}", r=105, deg=group_center_deg, adjust_rotation=True)

fig = circos.plotfig()
HTML(pio.to_html(fig, include_plotlyjs="cdn"))

from pycirclizely import Circos from pycirclizely.utils import ColorCycler, calc_group_spaces sectors = {name: 10 for name in "ABCDEFGHIJ"} group1, group2, group3 = list("ABCD"), list("EFG"), list("HIJ") # Calculate appropriate group between/within spaces # In this example, 10 sectors are displayed as groups dividied into [4, 3, 3] spaces = calc_group_spaces([4, 3, 3], space_bw_group=15, space_in_group=2) circos = Circos(sectors, space=spaces) # Plot sector track color_cycler = ColorCycler("Set3") for sector in circos.sectors: track = sector.add_track(r_lim=(85, 90)) track.axis(fillcolor=color_cycler.get_color()) track.text(sector.name) # Plot group sectors range color_cycler = ColorCycler("T10") for idx, group in enumerate((group1, group2, group3), 1): group_deg_lim = circos.get_group_sectors_deg_lim(group) circos.rect( r_lim=(97, 100), deg_lim=group_deg_lim, fillcolor=color_cycler.get_color(), line=dict(color="black", width=0.5), ) group_center_deg = sum(group_deg_lim) / 2 circos.text(f"Group{idx}", r=105, deg=group_center_deg, adjust_rotation=True) fig = circos.plotfig() HTML(pio.to_html(fig, include_plotlyjs="cdn"))

Out[3]:

Anti-clockwise¶

pyCirclize sets the coordinate direction of each sector as clockwise by default. Users can set the coordinate direction of any sector to anti-clockwise with sector2clockwise option when initializing Circos instance.

In [4]:

from pycirclizely import Circos

sectors = dict(A1=18000, A2=13000, A3=6000, A4=5000, B3=12000, B2=13000, B1=15000)
circos = Circos(
    sectors,
    space=3,
    # Set (B1, B2, B3) sector coordinate direction as anti-clockwise
    sector2clockwise=dict(B1=False, B2=False, B3=False),
)

for sector in circos.sectors:
    # Plot track
    color = "orange" if sector.name.startswith("A") else "skyblue"
    track = sector.add_track((94, 100), r_pad_ratio=0.1)
    track.axis(fillcolor=color)
    track.text(sector.name)
    # Plot xticks
    major_interval, minor_interval = 5000, 1000
    track.xticks_by_interval(
        major_interval,
        label_orientation="vertical",
        label_formatter=lambda v: f"{v / 1000:.0f} Kb",
    )
    track.xticks_by_interval(minor_interval, tick_length=1, show_label=False)

# Plot links
circos.link(("A1", 0, 10000), ("B1", 0, 10000))
circos.link(("A1", 18000, 13000), ("B1", 10000, 15000), fillcolor="tomato")
circos.link(("A2", 0, 13000), ("B2", 0, 13000))
circos.link(("A3", 0, 6000), ("B3", 6000, 12000))
circos.link(("A4", 0, 5000), ("B3", 0, 5000))

fig = circos.plotfig()
HTML(pio.to_html(fig, include_plotlyjs="cdn"))

from pycirclizely import Circos sectors = dict(A1=18000, A2=13000, A3=6000, A4=5000, B3=12000, B2=13000, B1=15000) circos = Circos( sectors, space=3, # Set (B1, B2, B3) sector coordinate direction as anti-clockwise sector2clockwise=dict(B1=False, B2=False, B3=False), ) for sector in circos.sectors: # Plot track color = "orange" if sector.name.startswith("A") else "skyblue" track = sector.add_track((94, 100), r_pad_ratio=0.1) track.axis(fillcolor=color) track.text(sector.name) # Plot xticks major_interval, minor_interval = 5000, 1000 track.xticks_by_interval( major_interval, label_orientation="vertical", label_formatter=lambda v: f"{v / 1000:.0f} Kb", ) track.xticks_by_interval(minor_interval, tick_length=1, show_label=False) # Plot links circos.link(("A1", 0, 10000), ("B1", 0, 10000)) circos.link(("A1", 18000, 13000), ("B1", 10000, 15000), fillcolor="tomato") circos.link(("A2", 0, 13000), ("B2", 0, 13000)) circos.link(("A3", 0, 6000), ("B3", 6000, 12000)) circos.link(("A4", 0, 5000), ("B3", 0, 5000)) fig = circos.plotfig() HTML(pio.to_html(fig, include_plotlyjs="cdn"))

Out[4]:

Colorbar¶

Users can easily plot colorbars with circos.colorbar() method.

In [5]:

import numpy as np

from pycirclizely import Circos

np.random.seed(0)

# Initialize Circos instance
circos = Circos(sectors=dict(data=100), start=90)
sector = circos.sectors[0]

# Plot heatmap track1 (cmap="RdBu_r")
track1 = sector.add_track((85, 100))
track1.axis()
vmin1, vmax1, cmap1 = 0, 100, "RdBu_r"
matrix1 = np.random.randint(vmin1, vmax1, (5, 100))

# Create first colorbar (vertical on the right)
coloraxis1 = circos.colorbar(
    vmin=vmin1,
    vmax=vmax1,
    cmap=cmap1,
    thicknessmode="pixels",
    thickness=15,
    lenmode="pixels",
    len=300,
    yanchor="middle",
    y=0.5,
    xanchor="left",
    x=1.0,
    ticks="outside",
)

# Apply coloraxis to heatmap
track1.heatmap(matrix1, cmap=cmap1, vmin=vmin1, vmax=vmax1, coloraxis=coloraxis1)

# Plot heatmap track2 (cmap="Viridis")
track2 = sector.add_track((65, 80))
track2.axis()
vmin2, vmax2, cmap2 = -200, 200, "Viridis"
matrix2 = np.random.randint(vmin2, vmax2, (3, 100))

# Create second colorbar (horizontal at bottom)
coloraxis2 = circos.colorbar(
    vmin=vmin2,
    vmax=vmax2,
    cmap=cmap2,
    title=dict(
        text="Colorbar in center", font=dict(size=16, color="blue"), side="bottom"
    ),
    thicknessmode="pixels",
    thickness=15,
    lenmode="pixels",
    len=250,
    yanchor="bottom",
    y=0.4,
    xanchor="center",
    x=0.5,
    orientation="h",
    tickfont=dict(size=12, color="red"),
)

# Apply coloraxis to second heatmap
track2.heatmap(matrix2, cmap=cmap2, vmin=vmin2, vmax=vmax2, coloraxis=coloraxis2)

fig = circos.plotfig()
HTML(pio.to_html(fig, include_plotlyjs="cdn"))

import numpy as np from pycirclizely import Circos np.random.seed(0) # Initialize Circos instance circos = Circos(sectors=dict(data=100), start=90) sector = circos.sectors[0] # Plot heatmap track1 (cmap="RdBu_r") track1 = sector.add_track((85, 100)) track1.axis() vmin1, vmax1, cmap1 = 0, 100, "RdBu_r" matrix1 = np.random.randint(vmin1, vmax1, (5, 100)) # Create first colorbar (vertical on the right) coloraxis1 = circos.colorbar( vmin=vmin1, vmax=vmax1, cmap=cmap1, thicknessmode="pixels", thickness=15, lenmode="pixels", len=300, yanchor="middle", y=0.5, xanchor="left", x=1.0, ticks="outside", ) # Apply coloraxis to heatmap track1.heatmap(matrix1, cmap=cmap1, vmin=vmin1, vmax=vmax1, coloraxis=coloraxis1) # Plot heatmap track2 (cmap="Viridis") track2 = sector.add_track((65, 80)) track2.axis() vmin2, vmax2, cmap2 = -200, 200, "Viridis" matrix2 = np.random.randint(vmin2, vmax2, (3, 100)) # Create second colorbar (horizontal at bottom) coloraxis2 = circos.colorbar( vmin=vmin2, vmax=vmax2, cmap=cmap2, title=dict( text="Colorbar in center", font=dict(size=16, color="blue"), side="bottom" ), thicknessmode="pixels", thickness=15, lenmode="pixels", len=250, yanchor="bottom", y=0.4, xanchor="center", x=0.5, orientation="h", tickfont=dict(size=12, color="red"), ) # Apply coloraxis to second heatmap track2.heatmap(matrix2, cmap=cmap2, vmin=vmin2, vmax=vmax2, coloraxis=coloraxis2) fig = circos.plotfig() HTML(pio.to_html(fig, include_plotlyjs="cdn"))

Out[5]:

Stacked Bar¶

Users can easily plot stacked bar chart from matrix dataframe with row and column names. Vertical and horizontal stacked bar chart can be plotted using track.stacked_bar() and track.stacked_barh() methods, respectively.

In [6]:

import numpy as np
import pandas as pd

from pycirclizely import Circos

np.random.seed(0)

# Generate matrix data for stacked bar plot
row_num, col_num = 12, 6
matrix = np.random.randint(5, 20, (row_num, col_num))
row_names = [f"R{i}" for i in range(row_num)]
col_names = [f"group{i}" for i in range(col_num)]
table_df = pd.DataFrame(matrix, index=row_names, columns=col_names)
print(table_df)

# Initialize Circos sector & track
circos = Circos(sectors=dict(bar=len(table_df.index)))
sector = circos.sectors[0]
track = sector.add_track((50, 100))
track.grid()

# Plot stacked bar
sb_table = track.stacked_bar(table_df, width=0.6, cmap="Set3")
x_list = sb_table.calc_bar_label_x_list(track.size)
track.xticks(
    x=x_list,
    labels=sb_table.row_names,
    outer=False,
    tick_length=0,
    label_margin=2,
    label_orientation="horizontal",
    text_kws=dict(font=dict(size=12)),
)

fig = circos.plotfig()
HTML(pio.to_html(fig, include_plotlyjs="cdn"))

import numpy as np import pandas as pd from pycirclizely import Circos np.random.seed(0) # Generate matrix data for stacked bar plot row_num, col_num = 12, 6 matrix = np.random.randint(5, 20, (row_num, col_num)) row_names = [f"R{i}" for i in range(row_num)] col_names = [f"group{i}" for i in range(col_num)] table_df = pd.DataFrame(matrix, index=row_names, columns=col_names) print(table_df) # Initialize Circos sector & track circos = Circos(sectors=dict(bar=len(table_df.index))) sector = circos.sectors[0] track = sector.add_track((50, 100)) track.grid() # Plot stacked bar sb_table = track.stacked_bar(table_df, width=0.6, cmap="Set3") x_list = sb_table.calc_bar_label_x_list(track.size) track.xticks( x=x_list, labels=sb_table.row_names, outer=False, tick_length=0, label_margin=2, label_orientation="horizontal", text_kws=dict(font=dict(size=12)), ) fig = circos.plotfig() HTML(pio.to_html(fig, include_plotlyjs="cdn"))

     group0  group1  group2  group3  group4  group5
R0       17      10       5       8      16       8
R1       12      14       8      10       7       9
R2       12      11      13      13      17      15
R3        6      11      12      12      19      13
R4        6      10      14      18      13      14
R5        9       8       5       8      10      19
R6        5       7       8      13       6       8
R7       18       8       8      19      12       5
R8        6      14      14       5      15       9
R9       12       8      19      16       7      12
R10      17       7       5       5       9      10
R11      10      11      13       9       6       9

Out[6]:

In [7]:

import numpy as np
import pandas as pd

from pycirclizely import Circos
from pycirclizely.parser import StackedBarTable

np.random.seed(0)

# Generate & load matrix data for horizontal stacked bar plot
row_names = list("ABCDEF")
col_names = ["group1", "group2", "group3", "group4", "group5", "group6"]
matrix = np.random.randint(5, 20, (len(row_names), len(col_names)))
table_df = pd.DataFrame(matrix, index=row_names, columns=col_names)
sb_table = StackedBarTable(table_df)
print(table_df)

# Initialize Circos sector & track (0 <= range <= 270)
circos = Circos(sectors=dict(bar=sb_table.row_sum_vmax), start=0, end=270)
sector = circos.sectors[0]
track = sector.add_track((30, 100))
track.axis(fillcolor="lightgrey", line=dict(color="black"), opacity=0.5)

# Plot horizontal stacked bar & label & xticks
track.stacked_barh(sb_table.dataframe, cmap="T10", width=0.6)
label_r_list = sb_table.calc_barh_label_r_list(track.r_plot_lim)
for label_r, row_name in zip(label_r_list, sb_table.row_names):
    track.text(f"{row_name} ", x=0, r=label_r, xanchor="right")
track.xticks_by_interval(interval=5)
track.xticks_by_interval(interval=1, tick_length=1, show_label=False)

fig = circos.plotfig()
HTML(pio.to_html(fig, include_plotlyjs="cdn"))

import numpy as np import pandas as pd from pycirclizely import Circos from pycirclizely.parser import StackedBarTable np.random.seed(0) # Generate & load matrix data for horizontal stacked bar plot row_names = list("ABCDEF") col_names = ["group1", "group2", "group3", "group4", "group5", "group6"] matrix = np.random.randint(5, 20, (len(row_names), len(col_names))) table_df = pd.DataFrame(matrix, index=row_names, columns=col_names) sb_table = StackedBarTable(table_df) print(table_df) # Initialize Circos sector & track (0 <= range <= 270) circos = Circos(sectors=dict(bar=sb_table.row_sum_vmax), start=0, end=270) sector = circos.sectors[0] track = sector.add_track((30, 100)) track.axis(fillcolor="lightgrey", line=dict(color="black"), opacity=0.5) # Plot horizontal stacked bar & label & xticks track.stacked_barh(sb_table.dataframe, cmap="T10", width=0.6) label_r_list = sb_table.calc_barh_label_r_list(track.r_plot_lim) for label_r, row_name in zip(label_r_list, sb_table.row_names): track.text(f"{row_name} ", x=0, r=label_r, xanchor="right") track.xticks_by_interval(interval=5) track.xticks_by_interval(interval=1, tick_length=1, show_label=False) fig = circos.plotfig() HTML(pio.to_html(fig, include_plotlyjs="cdn"))

   group1  group2  group3  group4  group5  group6
A      17      10       5       8      16       8
B      12      14       8      10       7       9
C      12      11      13      13      17      15
D       6      11      12      12      19      13
E       6      10      14      18      13      14
F       9       8       5       8      10      19

Out[7]:

Appendix¶

1. Clock¶

In [8]:

import numpy as np

from pycirclizely import Circos

circos = Circos(sectors={"clock": 12})
sector = circos.sectors[0]

# Plot outer line & xticks
track = sector.add_track(r_lim=(100, 100))
major_xticks = np.arange(0, 12, 1) + 1
track.xticks(major_xticks, outer=False, show_bottom_line=True)
minor_xticks = np.arange(0, 12, 0.2)
track.xticks(minor_xticks, outer=False, tick_length=1)

# Plot 1-12 hour characters
for x in major_xticks:
    track.text(str(x), x=x, r=93, font=dict(size=15), adjust_rotation=False)

# Plot clock hands (hour, minute, second)
sector.line(r=(0, 40), start=8, end=8, line=dict(width=3))
sector.line(r=(0, 70), start=0, end=0, line=dict(width=1.5))
sector.line(r=(0, 80), start=5, end=5, line=dict(width=0.5, color="red"))

fig = circos.plotfig()
HTML(pio.to_html(fig, include_plotlyjs="cdn"))

import numpy as np from pycirclizely import Circos circos = Circos(sectors={"clock": 12}) sector = circos.sectors[0] # Plot outer line & xticks track = sector.add_track(r_lim=(100, 100)) major_xticks = np.arange(0, 12, 1) + 1 track.xticks(major_xticks, outer=False, show_bottom_line=True) minor_xticks = np.arange(0, 12, 0.2) track.xticks(minor_xticks, outer=False, tick_length=1) # Plot 1-12 hour characters for x in major_xticks: track.text(str(x), x=x, r=93, font=dict(size=15), adjust_rotation=False) # Plot clock hands (hour, minute, second) sector.line(r=(0, 40), start=8, end=8, line=dict(width=3)) sector.line(r=(0, 70), start=0, end=0, line=dict(width=1.5)) sector.line(r=(0, 80), start=5, end=5, line=dict(width=0.5, color="red")) fig = circos.plotfig() HTML(pio.to_html(fig, include_plotlyjs="cdn"))

Out[8]:

2. Dartboard¶

In [9]:

from pycirclizely import Circos

points = [20, 1, 18, 4, 13, 6, 10, 15, 2, 17, 3, 19, 7, 16, 8, 11, 14, 9, 12, 5]
sectors = {str(p): 1 for p in points}
circos = Circos(sectors, space=0, start=-9, end=351)

red_or_green = ("red", "green")
black_or_white = ("black", "white")

circos.rect(r_lim=(85, 100), fillcolor="black")
for idx, sector in enumerate(circos.sectors):
    sector.text(
        sector.name, r=92.5, font=dict(color="white", size=12), adjust_rotation=False
    )
    color_idx = idx % 2
    sector.rect(
        r_lim=(80, 85),
        fillcolor=red_or_green[color_idx],
        line=dict(color="lightgrey", width=1),
    )
    sector.rect(
        r_lim=(52.5, 80),
        fillcolor=black_or_white[color_idx],
        line=dict(color="lightgrey", width=1),
    )
    sector.rect(
        r_lim=(47.5, 52.5),
        fillcolor=red_or_green[color_idx],
        line=dict(color="lightgrey", width=1),
    )
    sector.rect(
        r_lim=(10, 47.5),
        fillcolor=black_or_white[color_idx],
        line=dict(color="lightgrey", width=1),
    )
circos.rect(r_lim=(5, 10), fillcolor="green", line=dict(width=0))
circos.rect(r_lim=(0, 5), fillcolor="red", line=dict(width=0))
circos.line(r=5, line=dict(color="lightgrey", width=1))

fig = circos.plotfig()
HTML(pio.to_html(fig, include_plotlyjs="cdn"))

from pycirclizely import Circos points = [20, 1, 18, 4, 13, 6, 10, 15, 2, 17, 3, 19, 7, 16, 8, 11, 14, 9, 12, 5] sectors = {str(p): 1 for p in points} circos = Circos(sectors, space=0, start=-9, end=351) red_or_green = ("red", "green") black_or_white = ("black", "white") circos.rect(r_lim=(85, 100), fillcolor="black") for idx, sector in enumerate(circos.sectors): sector.text( sector.name, r=92.5, font=dict(color="white", size=12), adjust_rotation=False ) color_idx = idx % 2 sector.rect( r_lim=(80, 85), fillcolor=red_or_green[color_idx], line=dict(color="lightgrey", width=1), ) sector.rect( r_lim=(52.5, 80), fillcolor=black_or_white[color_idx], line=dict(color="lightgrey", width=1), ) sector.rect( r_lim=(47.5, 52.5), fillcolor=red_or_green[color_idx], line=dict(color="lightgrey", width=1), ) sector.rect( r_lim=(10, 47.5), fillcolor=black_or_white[color_idx], line=dict(color="lightgrey", width=1), ) circos.rect(r_lim=(5, 10), fillcolor="green", line=dict(width=0)) circos.rect(r_lim=(0, 5), fillcolor="red", line=dict(width=0)) circos.line(r=5, line=dict(color="lightgrey", width=1)) fig = circos.plotfig() HTML(pio.to_html(fig, include_plotlyjs="cdn"))

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In [ ]: