Merge pull request #63 from moshi4/develop

Bump to v1.4.0

.github/workflows/ci.yml

@@ -27,11 +27,11 @@ jobs:
       - name: Install dependencies
         run: pip install -e . pytest pytest-cov ruff
 
-      - name: Run ruff format check
-        run: ruff format --check --diff
-
       - name: Run ruff lint check
         run: ruff check --diff
 
+      - name: Run ruff format check
+        run: ruff format --check --diff
+
       - name: Run pytest
-        run: pytest tests --tb=line --cov=src --cov-report=xml --cov-report=term
+        run: pytest

.pre-commit-config.yaml

@@ -0,0 +1,11 @@
+# See https://pre-commit.com for more information
+# See https://pre-commit.com/hooks.html for more hooks
+repos:
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.3.1
+    hooks:
+      - id: ruff
+        name: ruff lint check
+        args: [--fix]
+      - id: ruff-format
+        name: ruff format check

README.md

@@ -46,6 +46,7 @@ API usage is described in each of the following sections in the [document](https
 - [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/)
 - [Phylogenetic Tree](https://moshi4.github.io/pyCirclize/phylogenetic_tree/)
 - [Plot Tips](https://moshi4.github.io/pyCirclize/plot_tips/)
@@ -125,8 +126,8 @@ r_cds_track.genomic_features(r_cds_feats, plotstyle="arrow", fc="skyblue", lw=0.
 # Plot 'gene' qualifier label if exists
 labels, label_pos_list = [], []
 for feat in gbk.extract_features("CDS"):
-    start = int(str(feat.location.start))
-    end = int(str(feat.location.end))
+    start = int(feat.location.start)
+    end = int(feat.location.end)
     label_pos = (start + end) / 2
     gene_name = feat.qualifiers.get("gene", [None])[0]
     if gene_name is not None:
@@ -223,6 +224,39 @@ 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)  
+
 ## Not Implemented Features
 
 List of features implemented in other Circos plotting tools but not yet implemented in pyCirclize.
@@ -231,7 +265,8 @@ I may implement them when I feel like it.
 - Plot histogram
 - Plot boxplot
 - Plot violin
-- Label position auto adjustment
+- Plot curved text
+- Adjust overlap label position
 
 ## Star History
 

docs/getting_started.ipynb

@@ -502,6 +502,7 @@
     "If you are interested in the contents of the following sections, you may want to look at them next.\n",
     "\n",
     "- [Chord Diagram](../chord_diagram/)\n",
+    "- [Radar Chart](../radar_chart/)\n",
     "- [Circos Plot (Genomics)](../circos_plot/)\n",
     "- [Phylogenetic Tree](../phylogenetic_tree/)"
    ]

docs/index.md

@@ -37,6 +37,7 @@ API usage is described in each of the following sections.
 - [Getting Started](./getting_started/)
 - [Plot API Example](./plot_api_example/)
 - [Chord Diagram](./chord_diagram/)
+- [Radar Chart](./radar_chart/)
 - [Circos Plot (Genomics)](./circos_plot/)
 - [Phylogenetic Tree](./phylogenetic_tree/)
 - [Plot Tips](./plot_tips/)

mkdocs.yml

@@ -13,6 +13,7 @@ nav:
   - Getting Started: getting_started.ipynb
   - Plot API Example: plot_api_example.ipynb
   - Chord Diagram: chord_diagram.ipynb
+  - Radar Chart: radar_chart.ipynb
   - Circos Plot (Genomics): circos_plot.ipynb
   - Phylogenetic Tree: phylogenetic_tree.ipynb
   - Plot Tips: plot_tips.ipynb

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "pyCirclize"
-version = "1.3.0"
+version = "1.4.0"
 description = "Circular visualization in Python"
 authors = ["moshi4"]
 license = "MIT"
@@ -23,7 +23,7 @@ include = ["tests"]
 
 [tool.pytest.ini_options]
 minversion = "6.0"
-addopts = "--cov=src --tb=line --cov-report=xml --cov-report=term"
+addopts = "--cov=src --tb=long -vv --cov-report=xml --cov-report=term"
 testpaths = ["tests"]
 
 [tool.ruff]
@@ -57,12 +57,13 @@ convention = "numpy"
 [tool.poetry.dependencies]
 python = "^3.8"
 matplotlib = ">=3.5.2"
-biopython = ">=1.79"
+biopython = ">=1.80"
 numpy = ">=1.21.1"
 pandas = ">=1.3.5"
 
 [tool.poetry.group.dev.dependencies]
 ruff = ">=0.1.6"
+pre-commit = ">=3.5.0"
 pytest = ">=7.1.2"
 pytest-cov = ">=4.0.0"
 ipykernel = ">=6.13.0"

src/pycirclize/__init__.py

@@ -1,6 +1,6 @@
 from pycirclize.circos import Circos
 
-__version__ = "1.3.0"
+__version__ = "1.4.0"
 
 __all__ = [
     "Circos",

src/pycirclize/circos.py

@@ -10,6 +10,7 @@
 from typing import Any, Callable
 
 import matplotlib.pyplot as plt
+import numpy as np
 import pandas as pd
 from Bio.Phylo.BaseTree import Tree
 from matplotlib.axes import Axes
@@ -21,7 +22,7 @@
 from matplotlib.projections.polar import PolarAxes
 
 from pycirclize import config, utils
-from pycirclize.parser import Bed, Matrix
+from pycirclize.parser import Bed, Matrix, RadarTable
 from pycirclize.patches import (
     ArcLine,
     ArcRectangle,
@@ -174,6 +175,154 @@ def ax(self) -> PolarAxes:
     # Public Method
     ############################################################
 
+    @staticmethod
+    def radar_chart(
+        table: str | Path | pd.DataFrame | RadarTable,
+        *,
+        r_lim: tuple[float, float] = (0, 100),
+        vmax: float = 100,
+        fill: bool = True,
+        marker_size: int = 0,
+        bg_color: str | None = "#eeeeee80",
+        circular: bool = False,
+        cmap: str | dict[str, str] = "Set2",
+        show_grid_label: bool = True,
+        grid_interval_ratio: float | None = 0.2,
+        grid_line_kws: dict[str, Any] | None = None,
+        grid_label_kws: dict[str, Any] | None = None,
+        grid_label_formatter: Callable[[float], str] | None = None,
+        label_kws_handler: Callable[[str], dict[str, Any]] | None = None,
+        line_kws_handler: Callable[[str], dict[str, Any]] | None = None,
+        marker_kws_handler: Callable[[str], dict[str, Any]] | None = None,
+    ) -> Circos:
+        """Plot radar chart
+
+        Parameters
+        ----------
+        table : str | Path | pd.DataFrame | RadarTable
+            Table file or Table dataframe or RadarTable instance
+        r_lim : tuple[float, float], optional
+            Radar chart radius limit region (0 - 100)
+        vmax : float, optional
+            Max value
+        fill : bool, optional
+            If True, fill color of radar chart.
+        marker_size : int, optional
+            Marker size
+        bg_color : str | None, optional
+            Background color
+        circular : bool, optional
+            If True, plot with circular style.
+        cmap : str | dict[str, str], optional
+            Colormap assigned to each target row(index) in table.
+            User can set matplotlib's colormap (e.g. `tab10`, `Set2`) or
+            target_name -> color dict (e.g. `dict(A="red", B="blue", C="green", ...)`)
+        show_grid_label : bool, optional
+            If True, show grid label.
+        grid_interval_ratio : float | None, optional
+            Grid interval ratio (0.0 - 1.0)
+        grid_line_kws : dict[str, Any] | None, optional
+            Keyword arguments passed to `track.line()` method
+            (e.g. `dict(color="black", ls="dotted", lw=1.0, ...)`)
+        grid_label_kws : dict[str, Any] | None, optional
+            Keyword arguments passed to `track.text()` method
+            (e.g. `dict(size=12, color="red", ...)`)
+        grid_label_formatter : Callable[[float], str] | None, optional
+            User-defined function to format grid label (e.g. `lambda v: f"{v:.1f}%"`).
+        label_kws_handler : Callable[[str], dict[str, Any]] | None, optional
+            Handler function for keyword arguments passed to `track.text()` method.
+            Handler function takes each column name of table as an argument.
+        line_kws_handler : Callable[[str], dict[str, Any]] | None, optional
+            Handler function for keyword arguments passed to `track.line()` method.
+            Handler function takes each row(index) name of table as an argument.
+        marker_kws_handler : Callable[[str], dict[str, Any]] | None, optional
+            Handler function for keyword arguments passed to `track.scatter()` method.
+            Handler function takes each row(index) name of table as an argument.
+
+        Returns
+        -------
+        circos : Circos
+            Circos instance initialized for radar chart
+        """
+        # Setup default properties
+        grid_line_kws = {} if grid_line_kws is None else deepcopy(grid_line_kws)
+        for k, v in dict(color="grey", ls="dashed", lw=0.5).items():
+            grid_line_kws.setdefault(k, v)
+
+        grid_label_kws = {} if grid_label_kws is None else deepcopy(grid_label_kws)
+        for k, v in dict(color="dimgrey", size=10, ha="left", va="top").items():
+            grid_label_kws.setdefault(k, v)
+
+        # Initialize circos for radar chart
+        radar_table = table if isinstance(table, RadarTable) else RadarTable(table)
+        circos = Circos(dict(radar=radar_table.col_num))
+        sector = circos.sectors[0]
+        track = sector.add_track(r_lim)
+        x = np.arange(radar_table.col_num + 1)
+
+        # Plot background color
+        if bg_color:
+            track.fill_between(x, [vmax] * len(x), arc=circular, color=bg_color)
+
+        # Plot grid line
+        if grid_interval_ratio:
+            if not 0 < grid_interval_ratio <= 1.0:
+                raise ValueError(f"{grid_interval_ratio=} is invalid.")
+            # Plot horizontal grid line & label
+            stop, step = vmax + (vmax / 1000), vmax * grid_interval_ratio
+            for v in np.arange(0, stop, step):
+                track.line(x, [v] * len(x), vmax=vmax, arc=circular, **grid_line_kws)
+                if show_grid_label:
+                    r = track._y_to_r(v, 0, vmax)
+                    # Format grid label
+                    if grid_label_formatter:
+                        text = grid_label_formatter(v)
+                    else:
+                        v = float(f"{v:.9f}")  # Correct rounding error
+                        text = f"{v:.0f}" if math.isclose(int(v), float(v)) else str(v)
+                    track.text(text, 0, r, **grid_label_kws)
+            # Plot vertical grid line
+            for p in x[:-1]:
+                track.line([p, p], [0, vmax], vmax=vmax, **grid_line_kws)
+
+        # Plot radar charts
+        if isinstance(cmap, str):
+            row_name2color = radar_table.get_row_name2color(cmap)
+        else:
+            row_name2color = cmap
+        for row_name, values in radar_table.row_name2values.items():
+            y = values + [values[0]]
+            color = row_name2color[row_name]
+            line_kws = line_kws_handler(row_name) if line_kws_handler else {}
+            line_kws.setdefault("lw", 1.0)
+            line_kws.setdefault("label", row_name)
+            track.line(x, y, vmax=vmax, arc=False, color=color, **line_kws)
+            if marker_size > 0:
+                marker_kws = marker_kws_handler(row_name) if marker_kws_handler else {}
+                marker_kws.setdefault("marker", "o")
+                marker_kws.setdefault("zorder", 2)
+                marker_kws.update(s=marker_size**2)
+                track.scatter(x, y, vmax=vmax, color=color, **marker_kws)
+            if fill:
+                track.fill_between(x, y, vmax=vmax, arc=False, color=color, alpha=0.5)
+
+        # Plot column names
+        for idx, col_name in enumerate(radar_table.col_names):
+            deg = 360 * (idx / sector.size)
+            label_kws = label_kws_handler(col_name) if label_kws_handler else {}
+            label_kws.setdefault("size", 12)
+            if math.isclose(deg, 0):
+                label_kws.update(va="bottom")
+            elif math.isclose(deg, 180):
+                label_kws.update(va="top")
+            elif 0 < deg < 180:
+                label_kws.update(ha="left")
+            elif 180 < deg < 360:
+                label_kws.update(ha="right")
+            track.text(col_name, idx, r=105, adjust_rotation=False, **label_kws)
+
+        return circos
+
     @staticmethod
     def initialize_from_matrix(
         matrix: str | Path | pd.DataFrame | Matrix,
@@ -302,6 +451,8 @@ def initialize_from_matrix(
 
         return circos
 
+    chord_diagram = initialize_from_matrix
+
     @staticmethod
     def initialize_from_tree(
         tree_data: str | Path | Tree,
@@ -837,6 +988,7 @@ def plotfig(
         dpi: int = 100,
         *,
         ax: PolarAxes | None = None,
+        figsize: tuple[float, float] = (8, 8),
     ) -> Figure:
         """Plot figure
 
@@ -846,6 +998,8 @@ def plotfig(
             Figure DPI
         ax : PolarAxes | None
             If None, figure and axes are newly created.
+        figsize : tuple[float, float], optional
+            Figure size
 
         Returns
         -------
@@ -854,7 +1008,7 @@ def plotfig(
         """
         if ax is None:
             # Initialize Figure & PolarAxes
-            fig, ax = self._initialize_figure(dpi=dpi)
+            fig, ax = self._initialize_figure(figsize=figsize, dpi=dpi)
         else:
             # Check PolarAxes or not
             if not isinstance(ax, PolarAxes):
@@ -891,6 +1045,7 @@ def savefig(
         savefile: str | Path,
         *,
         dpi: int = 100,
+        figsize: tuple[float, float] = (8, 8),
         pad_inches: float = 0.5,
     ) -> None:
         """Save figure to file
@@ -904,10 +1059,12 @@ def savefig(
             Save file (`*.png`|`*.jpg`|`*.svg`|`*.pdf`)
         dpi : int, optional
             DPI
+        figsize : tuple[float, float], optional
+            Figure size
         pad_inches : float, optional
             Padding inches
         """
-        fig = self.plotfig(dpi=dpi)
+        fig = self.plotfig(dpi=dpi, figsize=figsize)
         fig.savefig(
             fname=savefile,  # type: ignore
             dpi=dpi,