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pyCirclize

(★ 1,113)

Circular visualization in Python (Circos Plot, Chord Diagram, Radar Chart)

파일 탐색기

최종 버전 다운로드 (.zip)

- - ci.yml
  - publish_mkdocs.yml
  - publish_to_pypi.yml
- - circos.md
  - sector.md
  - track.md
  - treeviz.md
  - utils.md
- - example01.png
  - example02.png
  - example03.png
  - example04.png
  - example05.png
  - pyCirclize_gallery.png
  - pyCirclize_tooltip.gif
- chord_diagram.ipynb
- circos_plot.ipynb
- comparative_genomics.ipynb
- getting_started.ipynb
- index.md
- phylogenetic_tree.ipynb
- plot_api_example.ipynb
- plot_tips.ipynb
- radar_chart.ipynb
- - __init__.py
  - annotation.py
  - circos.py
  - config.py
  - patches.py
  - sector.py
  - tooltip.py
  - track.py
  - tree.py
  - typing.py
- - __init__.py
  - test_genbank.py
  - test_gff.py
  - test_matrix.py
  - test_table.py
- - __init__.py
  - test_dataset.py
  - test_helper.py
- __init__.py
- conftest.py
- test_circos.py
- test_plot.py
- test_sector.py
- test_track.py
.gitattributes
.gitignore
CITATION.cff
LICENSE
mkdocs.yml
prek.toml
pyproject.toml
README.md
uv.lock

# 설치 가이드

1. 코드 내려받기

git clone https://github.com/moshi4/pyCirclize

깃허브에서 프로젝트 코드 전체를 내 컴퓨터로 내려받습니다.

cd pyCirclize

방금 내려받은 프로젝트 폴더 안으로 이동합니다.

2. 공식 설치 스크립트

쉬움 추천

사전 준비물

Python 3 pip 명령어를 쓰려면 Python이 필요합니다.

pip install pycirclize[tooltip]

PyPI에 배포된 패키지를 바로 설치합니다. 소스 클론이 필요 없습니다.

pip install pycirclize

PyPI에 배포된 패키지를 바로 설치합니다. 소스 클론이 필요 없습니다.

✅ 설치 후 새 터미널을 열고, 프로그램의 버전 확인 명령(예: --version)으로 정상 설치됐는지 확인하세요.

이 레포의 README에 적힌 실제 명령어를 그대로 가져왔습니다.

3. Python

쉬움

사전 준비물

Git GitHub에서 프로젝트 코드를 내려받으려면 필요합니다.
Python 3 설치 시 'Add Python to PATH' 옵션을 꼭 체크하세요 (Windows).

pip install pycirclize[tooltip]

PyPI에 배포된 패키지를 바로 설치합니다. 소스 클론이 필요 없습니다.

pip install pycirclize

PyPI에 배포된 패키지를 바로 설치합니다. 소스 클론이 필요 없습니다.

✅ 에러 메시지 없이 실행되고 터미널에 안내 문구가 출력되면 정상입니다.

이 레포의 README에 적힌 실제 명령어를 그대로 가져왔습니다.

// repository documentation

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# pyCirclize: Circular visualization in Python

![Python3](https://img.shields.io/badge/Language-Python3-steelblue)
![OS](https://img.shields.io/badge/OS-_Windows_|_Mac_|_Linux-steelblue)
![License](https://img.shields.io/badge/License-MIT-steelblue)
[![Latest PyPI version](https://img.shields.io/pypi/v/pycirclize.svg)](https://pypi.python.org/pypi/pycirclize)
[![conda-forge](https://img.shields.io/conda/vn/conda-forge/pycirclize.svg?color=green)](https://anaconda.org/conda-forge/pycirclize)
[![CI](https://github.com/moshi4/pyCirclize/actions/workflows/ci.yml/badge.svg)](https://github.com/moshi4/pyCirclize/actions/workflows/ci.yml)

## Table of contents

- [Overview](#overview)
- [Installation](#installation)
- [API Usage](#api-usage)
- [Code Example](#code-example)
- [Tooltip Option](#tooltip-option)
- [Star History](#star-history)

## Overview

pyCirclize is a circular visualization python package implemented based on matplotlib.
This package is developed for the purpose of easily and beautifully plotting circular figure such as Circos Plot and Chord Diagram in Python.
In addition, useful genome and phylogenetic tree visualization methods for the bioinformatics field are also implemented.
pyCirclize was inspired by [circlize](https://github.com/jokergoo/circlize) and [pyCircos](https://github.com/ponnhide/pyCircos).
More detailed documentation is available [here](https://moshi4.github.io/pyCirclize/).

![pyCirclize_gallery.png](https://raw.githubusercontent.com/moshi4/pyCirclize/main/docs/images/pyCirclize_gallery.png)  
**Fig.1 pyCirclize example plot gallery**

## Installation

`Python 3.10 or later` is required for installation.

**Install PyPI package:**

pip install pycirclize

**Install conda-forge package:**

conda install -c conda-forge pycirclize

## API Usage

API usage is described in each of the following sections in the [document](https://moshi4.github.io/pyCirclize/).

- [Getting Started](https://moshi4.github.io/pyCirclize/getting_started/)
- [Plot API Example](https://moshi4.github.io/pyCirclize/plot_api_example/)
- [Chord Diagram](https://moshi4.github.io/pyCirclize/chord_diagram/)
- [Radar Chart](https://moshi4.github.io/pyCirclize/radar_chart/)
- [Circos Plot (Genomics)](https://moshi4.github.io/pyCirclize/circos_plot/)
- [Comparative Genomics](https://moshi4.github.io/pyCirclize/comparative_genomics/)
- [Phylogenetic Tree](https://moshi4.github.io/pyCirclize/phylogenetic_tree/)
- [Plot Tips](https://moshi4.github.io/pyCirclize/plot_tips/)

## Code Example

### 1. Circos Plot

```python
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 & random y values
    x = np.arange(sector.start, sector.end) + 0.5
    y = np.random.randint(0, 100, len(x))
    # Plot lines
    track1 = sector.add_track((80, 100), r_pad_ratio=0.1)
    track1.xticks_by_interval(interval=1)
    track1.axis()
    track1.line(x, y)
    # Plot points 
    track2 = sector.add_track((55, 75), r_pad_ratio=0.1)
    track2.axis()
    track2.scatter(x, y)
    # Plot bars
    track3 = sector.add_track((30, 50), r_pad_ratio=0.1)
    track3.axis()
    track3.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")

circos.savefig("example01.png")
```

![example01.png](https://raw.githubusercontent.com/moshi4/pyCirclize/main/docs/images/example01.png)

### 2. Circos Plot (Genomics)

```python
from pycirclize import Circos
from pycirclize.utils import fetch_genbank_by_accid
from pycirclize.parser import Genbank

# Download `NC_002483` E.coli plasmid genbank
gbk_fetch_data = fetch_genbank_by_accid("NC_002483")
gbk = Genbank(gbk_fetch_data)

# Initialize Circos instance with genome size
sectors = gbk.get_seqid2size()
space = 0 if len(sectors) == 1 else 2
circos = Circos(sectors, space=space)
circos.text(f"Escherichia coli K-12 plasmid F\n\n{gbk.name}", size=14)

seqid2features = gbk.get_seqid2features(feature_type="CDS")
for sector in circos.sectors:
    # Setup track for features plot
    f_cds_track = sector.add_track((95, 100))
    f_cds_track.axis(fc="lightgrey", ec="none", alpha=0.5)
    r_cds_track = sector.add_track((90, 95))
    r_cds_track.axis(fc="lightgrey", ec="none", alpha=0.5)
    # Plot forward/reverse strand CDS
    features = seqid2features[sector.name]
    for feature in features:
        if feature.location.strand == 1:
            f_cds_track.genomic_features(feature, plotstyle="arrow", fc="salmon", lw=0.5)
        else:
            r_cds_track.genomic_features(feature, plotstyle="arrow", fc="skyblue", lw=0.5)

# Plot 'gene' qualifier label if exists
    labels, label_pos_list = [], []
    for feature in features:
        start = int(feature.location.start)
        end = int(feature.location.end)
        label_pos = (start + end) / 2
        gene_name = feature.qualifiers.get("gene", [None])[0]
        if gene_name is not None:
            labels.append(gene_name)
            label_pos_list.append(label_pos)
            f_cds_track.annotate(label_pos, gene_name, label_size=6)

# Plot xticks (interval = 10 Kb)
    r_cds_track.xticks_by_interval(
        10000, outer=False, label_formatter=lambda v: f"{v/1000:.1f} Kb"
    )

circos.savefig("example02.png")
```

![example02.png](https://raw.githubusercontent.com/moshi4/pyCirclize/main/docs/images/example02.png)

### 3. Chord Diagram

```python
from pycirclize import Circos
import pandas as pd

# Create matrix dataframe (3 x 6)
row_names = ["F1", "F2", "F3"]
col_names = ["T1", "T2", "T3", "T4", "T5", "T6"]
matrix_data = [
    [10, 16, 7, 7, 10, 8],
    [4, 9, 10, 12, 12, 7],
    [17, 13, 7, 4, 20, 4],
]
matrix_df = pd.DataFrame(matrix_data, index=row_names, columns=col_names)

# Initialize Circos instance for chord diagram plot
circos = Circos.chord_diagram(
    matrix_df,
    space=5,
    cmap="tab10",
    label_kws=dict(size=12),
    link_kws=dict(ec="black", lw=0.5, direction=1),
)

circos.savefig("example03.png")
```

![example03.png](https://raw.githubusercontent.com/moshi4/pyCirclize/main/docs/images/example03.png)

### 4. Phylogenetic Tree

```python
from pycirclize import Circos
from pycirclize.utils import load_example_tree_file, ColorCycler
from matplotlib.lines import Line2D

# Initialize Circos from phylogenetic tree
tree_file = load_example_tree_file("large_example.nwk")
circos, tv = Circos.initialize_from_tree(
    tree_file,
    r_lim=(30, 100),
    leaf_label_size=5,
    line_kws=dict(color="lightgrey", lw=1.0),
)

# Define group-species dict for tree annotation
# In this example, set minimum species list to specify group's MRCA node
group_name2species_list = dict(
    Monotremata=["Tachyglossus_aculeatus", "Ornithorhynchus_anatinus"],
    Marsupialia=["Monodelphis_domestica", "Vombatus_ursinus"],
    Xenarthra=["Choloepus_didactylus", "Dasypus_novemcinctus"],
    Afrotheria=["Trichechus_manatus", "Chrysochloris_asiatica"],
    Euarchontes=["Galeopterus_variegatus", "Theropithecus_gelada"],
    Glires=["Oryctolagus_cuniculus", "Microtus_oregoni"],
    Laurasiatheria=["Talpa_occidentalis", "Mirounga_leonina"],
)

# Set tree line color & label color
ColorCycler.set_cmap("tab10")
group_name2color = {name: ColorCycler() for name in group_name2species_list.keys()}
for group_name, species_list in group_name2species_list.items():
    color = group_name2color[group_name]
    tv.set_node_line_props(species_list, color=color, apply_label_color=True)

# Plot figure & set legend on center
fig = circos.plotfig()
_ = circos.ax.legend(
    handles=[Line2D([], [], label=n, color=c) for n, c in group_name2color.items()],
    labelcolor=group_name2color.values(),
    fontsize=6,
    loc="center",
    bbox_to_anchor=(0.5, 0.5),
)
fig.savefig("example04.png")
```

![example04.png](https://raw.githubusercontent.com/moshi4/pyCirclize/main/docs/images/example04.png)

### 5. Radar Chart

```python
from pycirclize import Circos
import pandas as pd

# Create RPG jobs parameter dataframe (3 jobs, 7 parameters)
df = pd.DataFrame(
    data=[
        [80, 80, 80, 80, 80, 80, 80],
        [90, 20, 95, 95, 30, 30, 80],
        [60, 90, 20, 20, 100, 90, 50],
    ],
    index=["Hero", "Warrior", "Wizard"],
    columns=["HP", "MP", "ATK", "DEF", "SP.ATK", "SP.DEF", "SPD"],
)

# Initialize Circos instance for radar chart plot
circos = Circos.radar_chart(
    df,
    vmax=100,
    marker_size=6,
    grid_interval_ratio=0.2,
)

# Plot figure & set legend on upper right
fig = circos.plotfig()
_ = circos.ax.legend(loc="upper right", fontsize=10)
fig.savefig("example05.png")
```

![example05.png](https://raw.githubusercontent.com/moshi4/pyCirclize/main/docs/images/example05.png)

## Tooltip Option

pyCirclize supports tooltip display in jupyter using [ipympl](https://github.com/matplotlib/ipympl).
To enable tooltip, install pycirclize with ipympl and call `circos.plotfig(tooltip=True)` method.
Tooltip option is tested on jupyter notebooks in VScode and JupyterLab.

```shell
pip install pycirclize[tooltip]
# or
conda install -c conda-forge pycirclize ipympl
```

> [!WARNING]
> Interactive tooltip plots require live python kernel.
> Be aware that tooltips are not permanently enabled in the notebook after plotting.

![pyCirclize_tooltip.gif](https://raw.githubusercontent.com/moshi4/pyCirclize/main/docs/images/pyCirclize_tooltip.gif)

## Star History

[![Star History Chart](https://api.star-history.com/svg?repos=moshi4/pyCirclize&type=Date)](https://star-history.com/#moshi4/pyCirclize&Date)