python 环状图 (pycirclize)

# %% [markdown]
# # 环状图可视化
# 
# pyCirclize 的灵感来自 circlize 和 pyCircos。

# %%
## 安装 必要包
%pip install pycirclize

# %%
# 导入包
from pycirclize import Circos

# %% [markdown]
# ### 设置扇形
# 在圆形布局中设置扇区时需要每个数据的大小，也可以设置扇区之间的空间大小

# %%
# Initialize circos sectors
sectors = {"A": 10, "B": 15, "C": 12, "D": 20, "E": 15}
circos = Circos(sectors, space=5)

for sector in circos.sectors:
    # Plot sector axis & name text
    # fc="none"：表示填充颜色（face color）为 "none"，即不填充任何颜色。
    # ls="dashdot"：表示线型为虚实相间的点划线（dash-dot line style）。
    # lw=2：表示线宽为 2。
    # ec="black"：表示边框颜色（edge color）为黑色。
    # alpha=0.5：表示透明度为 0.5（范围为 0 到 1，0 表示完全透明，1 表示完全不透明）。
    sector.axis(fc="none", ls="dashdot", lw=2, ec="black", alpha=0.5)
    sector.text(f"Sector: {sector.name}={sector.size}", size=15)
    print(sector)
fig = circos.plotfig()


# %% [markdown]
# 可以自由设置圆形布局的起始和结束角度，范围从-360到360。以下代码是设置start=-270和end=30的示例

# %%
# Initialize circos sectors
sectors = {"A": 10, "B": 15, "C": 12, "D": 20, "E": 15}
circos = Circos(sectors, space=5, start=-270, end=30) # Set start-end degree ranges

for sector in circos.sectors:
    # Plot sector axis & name text
    sector.axis(fc="none", ls="dashdot", lw=2, ec="black", alpha=0.5)
    sector.text(f"Sector: {sector.name}={sector.size}", size=15)

fig = circos.plotfig()

# %% [markdown]
# ### Set Tracks
# 可以在扇区半径范围（0 - 100）内自由放置磁道。以下代码是在每个扇区放置 3 条磁道的示例

# %%
# Initialize circos sectors
sectors = {"A": 10, "B": 15, "C": 12, "D": 20, "E": 15}
circos = Circos(sectors, space=5)

for sector in circos.sectors:
    # Plot sector axis & name text
    sector.axis(fc="none", ls="dashdot", lw=2, ec="black", alpha=0.5)
    sector.text(f"Sector: {sector.name}={sector.size}", size=15)
    # Set Track01 (Radius: 75 - 100)
    track1 = sector.add_track((75, 100))
    track1.axis(fc="tomato", alpha=0.5)
    track1.text(track1.name)
    # Set Track02 (Radius: 45 - 70)
    track2 = sector.add_track((45, 70))
    track2.axis(fc="cyan", alpha=0.5)
    track2.text(track2.name)
    # Set Track03 (Radius: 15 - 40)
    track3 = sector.add_track((15, 40))
    track3.axis(fc="lime", alpha=0.5)
    track3.text(track3.name)

fig = circos.plotfig()

# %% [markdown]
# ## Plot Data on Track

# %%
import numpy as np
np.random.seed(0)

sectors = {"A": 10, "B": 15, "C": 12, "D": 20, "E": 15}
circos = Circos(sectors, space=5)
for sector in circos.sectors:
    # Plot sector name
    sector.text(f"Sector: {sector.name}", r=110, size=15)
    # Create x positions & randomized y values for data plotting
    x = np.arange(sector.start, sector.end) + 0.5
    y = np.random.randint(0, 100, len(x))
    # Plot line
    line_track = sector.add_track((75, 100), r_pad_ratio=0.1)
    line_track.axis()
    line_track.xticks_by_interval(1)
    line_track.line(x, y)
    # Plot points
    points_track = sector.add_track((45, 70), r_pad_ratio=0.1)
    points_track.axis()
    points_track.scatter(x, y)
    # Plot bar
    bar_track = sector.add_track((15, 40), r_pad_ratio=0.1)
    bar_track.axis()
    bar_track.bar(x, y)
    
fig = circos.plotfig()

# %% [markdown]
# 还可以按照如下方式在复杂的圆形布局中绘制更多数据

# %%
rect_track.size
i * rect_size, i * rect_size + rect_size

# %%
from pycirclize import Circos
from pycirclize.utils import ColorCycler
import numpy as np

np.random.seed(0)
ColorCycler.set_cmap("tab10")

sectors = {"A": 200, "B": 140, "C": 160}
sector_colors = {"A": "red", "B": "blue", "C": "green"}
circos = Circos(sectors, space=10, start=90, end=360, endspace=False)

for sector in circos.sectors:
    # Outer Track
    outer_track = sector.add_track((95, 100))
    outer_track.text(sector.name, color="white")
    outer_track.axis(fc=sector_colors[sector.name])
    # interval=10：表示刻度标记之间的间隔为 10。例如，如果数据范围是从 0 到 100，那么刻度标记会出现在 0、10、20、30 等位置。
    # label_orientation="vertical"：表示刻度标签的文字方向为垂直方向（vertical）。其他可能的值包括水平方向（horizontal）或其他自定义角度。
    outer_track.xticks_by_interval(interval=10, label_orientation="vertical")
    # Rectangle Track
    rect_track = sector.add_track((90, 95))
    rect_size = 10
    # 循环遍历 rect_track 的大小范围，将其划分为多个矩形区域。
    # rect_track.size：表示轨道的总长度或大小。
    # rect_size：表示每个矩形的固定宽度。
    # int(rect_track.size / rect_size)：计算可以划分的矩形数量（向下取整）
    for i in range(int(rect_track.size / rect_size)):
        # 定义当前矩形的起始位置 (x1) 和结束位置 (x2)
        # i * rect_size：当前矩形的起始位置，基于索引 i 和矩形宽度 rect_size 计算。
        # i * rect_size + rect_size：当前矩形的结束位置。
        x1, x2 = i * rect_size, i * rect_size + rect_size
        # 在 rect_track 上绘制一个矩形
        # x1, x2：矩形的起始和结束位置
        rect_track.rect(x1, x2, ec="black", lw=0.5, color=ColorCycler())
        # 在矩形中心添加文本标签。
        rect_track.text(str(i + 1), (x1 + x2) / 2, size=8, color="white")
    # Generate random x, y plot data
    x = np.arange(1, int(sector.size), 2)
    y = np.random.randint(0, 10, len(x))
    # Line Track
    line_track = sector.add_track((80, 90), r_pad_ratio=0.1)
    line_track.axis()
    line_track.line(x, y, color="blue")
    # Scatter Track
    scatter_track = sector.add_track((70, 80), r_pad_ratio=0.1)
    scatter_track.axis()
    scatter_track.bar(x, y, width=0.8, color="orange")
    # Bar Track
    bar_track = sector.add_track((60, 70), r_pad_ratio=0.1)
    bar_track.axis()
    bar_track.scatter(x, y, color="green", s=3)
    # Fill Track
    fill_track = sector.add_track((50, 60), r_pad_ratio=0.1)
    fill_track.axis()
    fill_track.fill_between(x, y, y2=0, fc="red", ec="black", lw=0.5, alpha=0.5)
    # Line + Bar + Scatter Track
    line_bar_scatter_track = sector.add_track((40, 50), r_pad_ratio=0.1)
    line_bar_scatter_track.axis()
    line_bar_scatter_track.line(x, y, color="blue")
    line_bar_scatter_track.bar(x, y, width=0.8, color="orange")
    line_bar_scatter_track.scatter(x, y, color="green", s=3)
    
    
# Plot text description
text_common_kws = dict(ha="left", va="center", size=8)
circos.text(" 01. Outer Track", r=97.5, color="black", **text_common_kws)
circos.text(" 02. Rectangle Track", r=92.5, color="grey", **text_common_kws)
circos.text(" 03. Line Track", r=85, color="blue", **text_common_kws)
circos.text(" 04. Bar Track", r=75, color="orange", **text_common_kws)
circos.text(" 05. Scatter Track", r=65, color="green", **text_common_kws)
circos.text(" 06. Fill between Track", r=55, color="red", **text_common_kws)
circos.text(" 07. Line + Bar + Scatter Track", r=45, color="purple", **text_common_kws)

fig = circos.plotfig()

# %% [markdown]
# ## Plot Link
# pyCirclize 实现了绘制扇区内或扇区间数据链接的功能。此功能使用户能够可视化数据之间的相互关系，例如网络和流

# %%
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)
    # 此方法用于在 track 对象上根据指定的间隔生成刻度标记（ticks）。
    # 刻度标记之间的间隔为 1
    track.xticks_by_interval(1)
    
# Plot links
circos.link(("A", 0, 1), ("A", 7, 8))
circos.link(("A", 1, 2), ("A", 7, 6))
circos.link(("A", 9, 10), ("B", 4, 3))
circos.link(("B", 5, 7), ("C", 6, 8))
circos.link(("B", 18, 16), ("B", 11, 13))
circos.link(("C", 1, 3), ("B", 2, 0))
circos.link(("C", 11.5, 14), ("A", 4, 3))

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 with 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
import numpy as np
np.random.seed(0)

# Initialize Circos sectors
sectors = {"A": 10, "B": 15, "C": 12, "D": 20, "E": 15}
circos = Circos(sectors, space=5)

for sector in circos.sectors:
    # Plot sector name
    sector.text(f"Sector: {sector.name}", r=110, size=15)
    # Create x positions & randomized y values
    x = np.arange(sector.start, sector.end) + 0.5
    y = np.random.randint(0, 100, len(x))
    # Plot line track
    line_track = sector.add_track((80, 100), r_pad_ratio=0.1)
    line_track.xticks_by_interval(interval=1)
    line_track.axis()
    line_track.line(x, y)
    # Plot points track
    points_track = sector.add_track((55, 75), r_pad_ratio=0.1)
    points_track.axis()
    points_track.scatter(x, y)
    # Plot bar track
    bar_track = sector.add_track((30, 50), r_pad_ratio=0.1)
    bar_track.axis()
    bar_track.bar(x, y)

# Plot links
circos.link(("A", 0, 3), ("B", 15, 12))
circos.link(("B", 0, 3), ("C", 7, 11), color="skyblue")
circos.link(("C", 2, 5), ("E", 15, 12), color="chocolate", direction=1)
circos.link(("D", 3, 5), ("D", 18, 15), color="lime", ec="black", lw=0.5, hatch="//", direction=2)
circos.link(("D", 8, 10), ("E", 2, 8), color="violet", ec="red", lw=1.0, ls="dashed")

fig = circos.plotfig()