Merge pull request #68 from moshi4/develop

Bump to v1.5.0

.pre-commit-config.yaml

@@ -2,7 +2,7 @@
 # See https://pre-commit.com/hooks.html for more hooks
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.3.1
+    rev: v0.4.4
     hooks:
       - id: ruff
         name: ruff lint check

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "pyCirclize"
-version = "1.4.0"
+version = "1.5.0"
 description = "Circular visualization in Python"
 authors = ["moshi4"]
 license = "MIT"

src/pycirclize/__init__.py

@@ -1,6 +1,6 @@
 from pycirclize.circos import Circos
 
-__version__ = "1.4.0"
+__version__ = "1.5.0"
 
 __all__ = [
     "Circos",

src/pycirclize/circos.py

@@ -40,21 +40,20 @@ class Circos:
 
     def __init__(
         self,
-        sectors: Mapping[str, int | float],
+        sectors: Mapping[str, int | float | tuple[float, float]],
         start: float = 0,
         end: float = 360,
         *,
         space: float | list[float] = 0,
         endspace: bool = True,
-        sector2start_pos: Mapping[str, int | float] | None = None,
         sector2clockwise: dict[str, bool] | None = None,
         show_axis_for_debug: bool = False,
     ):
         """
         Parameters
         ----------
-        sectors : Mapping[str, int | float]
-            Sector name & size dict
+        sectors : Mapping[str, int | float | tuple[float, float]]
+            Sector name & size (or range) dict
         start : float, optional
             Plot start degree (`-360 <= start < end <= 360`)
         end : float, optional
@@ -63,14 +62,11 @@ def __init__(
             Space degree(s) between sector
         endspace : bool, optional
             If True, insert space after the end sector
-        sector2start_pos : Mapping[str, int | float] | None, optional
-            Sector name & start position dict. By default, `start_pos=0`.
         sector2clockwise : dict[str, bool] | None, optional
             Sector name & clockwise bool dict. By default, `clockwise=True`.
         show_axis_for_debug : bool, optional
             Show axis for position check debugging (Developer option)
         """
-        sector2start_pos = {} if sector2start_pos is None else sector2start_pos
         sector2clockwise = {} if sector2clockwise is None else sector2clockwise
 
         # Check start-end degree range
@@ -100,19 +96,21 @@ def __init__(
                 """
             )[1:-1]
             raise ValueError(err_msg)
-        sector_total_size = sum(sectors.values())
+
+        sector2range = self._to_sector2range(sectors)
+        sector_total_size = sum([max(r) - min(r) for r in sector2range.values()])
 
         rad_pos = math.radians(start)
         self._sectors: list[Sector] = []
-        for idx, (sector_name, sector_size) in enumerate(sectors.items()):
+        for idx, (sector_name, sector_range) in enumerate(sector2range.items()):
+            sector_size = max(sector_range) - min(sector_range)
             sector_size_ratio = sector_size / sector_total_size
             deg_size = whole_deg_size_without_space * sector_size_ratio
             rad_size = math.radians(deg_size)
             rad_lim = (rad_pos, rad_pos + rad_size)
             rad_pos += rad_size + math.radians(space_list[idx])
-            start_pos = sector2start_pos.get(sector_name, 0)
             clockwise = sector2clockwise.get(sector_name, True)
-            sector = Sector(sector_name, sector_size, rad_lim, start_pos, clockwise)
+            sector = Sector(sector_name, sector_range, rad_lim, clockwise)
             self._sectors.append(sector)
 
         self._deg_lim = (start, end)
@@ -180,6 +178,7 @@ def radar_chart(
         table: str | Path | pd.DataFrame | RadarTable,
         *,
         r_lim: tuple[float, float] = (0, 100),
+        vmin: float = 0,
         vmax: float = 100,
         fill: bool = True,
         marker_size: int = 0,
@@ -203,6 +202,8 @@ def radar_chart(
             Table file or Table dataframe or RadarTable instance
         r_lim : tuple[float, float], optional
             Radar chart radius limit region (0 - 100)
+        vmin : float, optional
+            Min value
         vmax : float, optional
             Max value
         fill : bool, optional
@@ -244,6 +245,10 @@ def radar_chart(
         circos : Circos
             Circos instance initialized for radar chart
         """
+        if not vmin < vmax:
+            raise ValueError(f"vmax must be larger than vmin ({vmin=}, {vmax=})")
+        size = vmax - vmin
+
         # 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():
@@ -269,11 +274,12 @@ def radar_chart(
             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)
+            stop, step = vmax + (size / 1000), size * grid_interval_ratio
+            for v in np.arange(vmin, stop, step):
+                y = [v] * len(x)
+                track.line(x, y, vmin=vmin, vmax=vmax, arc=circular, **grid_line_kws)
                 if show_grid_label:
-                    r = track._y_to_r(v, 0, vmax)
+                    r = track._y_to_r(v, vmin, vmax)
                     # Format grid label
                     if grid_label_formatter:
                         text = grid_label_formatter(v)
@@ -283,7 +289,7 @@ def radar_chart(
                     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)
+                track.line([p, p], [vmin, vmax], vmin=vmin, vmax=vmax, **grid_line_kws)
 
         # Plot radar charts
         if isinstance(cmap, str):
@@ -296,15 +302,16 @@ def radar_chart(
             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)
+            track.line(x, y, vmin=vmin, 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)
+                track.scatter(x, y, vmin=vmin, vmax=vmax, color=color, **marker_kws)
             if fill:
-                track.fill_between(x, y, vmax=vmax, arc=False, color=color, alpha=0.5)
+                fill_kws = dict(arc=False, color=color, alpha=0.5)
+                track.fill_between(x, y, y2=vmin, vmin=vmin, vmax=vmax, **fill_kws)  # type:ignore
 
         # Plot column names
         for idx, col_name in enumerate(radar_table.col_names):
@@ -577,15 +584,13 @@ def initialize_from_bed(
             Circos instance initialized from BED file
         """
         records = Bed(bed_file).records
-        sectors = {rec.chr: rec.size for rec in records}
-        sector2start_pos = {rec.chr: rec.start for rec in records}
+        sectors = {rec.chr: (rec.start, rec.end) for rec in records}
         return Circos(
             sectors,
             start,
             end,
             space=space,
             endspace=endspace,
-            sector2start_pos=sector2start_pos,
             sector2clockwise=sector2clockwise,
         )
 
@@ -1098,6 +1103,23 @@ def _check_degree_range(self, start: float, end: float) -> None:
             err_msg = f"'end - start' must be less than {max_deg} ({start=}, {end=})"
             raise ValueError(err_msg)
 
+    def _to_sector2range(
+        self,
+        sectors: Mapping[str, int | float | tuple[float, float]],
+    ) -> dict[str, tuple[float, float]]:
+        """Convert sectors to sector2range"""
+        sector2range: dict[str, tuple[float, float]] = {}
+        for name, value in sectors.items():
+            if isinstance(value, (tuple, list)):
+                sector_start, sector_end = value
+                if not sector_start < sector_end:
+                    err_msg = f"{sector_end=} must be larger than {sector_start=}."
+                    raise ValueError(err_msg)
+                sector2range[name] = (sector_start, sector_end)
+            else:
+                sector2range[name] = (0, value)
+        return sector2range
+
     def _initialize_figure(
         self,
         figsize: tuple[float, float] = (8, 8),

src/pycirclize/parser/genbank.py

@@ -7,12 +7,16 @@
 from collections import defaultdict
 from io import StringIO, TextIOWrapper
 from pathlib import Path
+from typing import TYPE_CHECKING
 
 import numpy as np
 from Bio import SeqIO, SeqUtils
 from Bio.SeqFeature import Seq, SeqFeature, SimpleLocation
 from Bio.SeqRecord import SeqRecord
 
+if TYPE_CHECKING:
+    from numpy.typing import NDArray
+
 
 class Genbank:
     """Genbank Parser Class"""
@@ -56,11 +60,14 @@ def __init__(
         elif isinstance(self._gbk_source, (StringIO, TextIOWrapper)):
             self._name = self._records[0].name
         else:
-            raise NotImplementedError("Failed to get name.")
+            raise ValueError("Failed to get genbank name.")
 
         if min_range or max_range:
             warnings.warn("min_range & max_range is no longer used in Genbank parser.")
 
+        if len(self.records) == 0:
+            raise ValueError(f"Failed to parse {gbk_source} as Genbank file.")
+
     ############################################################
     # Property
     ############################################################
@@ -127,7 +134,7 @@ def calc_gc_skew(
         step_size: int | None = None,
         *,
         seq: str | None = None,
-    ) -> tuple[np.ndarray, np.ndarray]:
+    ) -> tuple[NDArray[np.int64], NDArray[np.float64]]:
         """Calculate GC skew in sliding window
 
         Parameters
@@ -141,7 +148,7 @@ def calc_gc_skew(
 
         Returns
         -------
-        gc_skew_result_tuple : tuple[np.ndarray, np.ndarray]
+        gc_skew_result_tuple : tuple[NDArray[np.int64], NDArray[np.float64]]
             Position list & GC skew list
         """
         pos_list, gc_skew_list = [], []
@@ -168,15 +175,18 @@ def calc_gc_skew(
                 skew = 0.0
             gc_skew_list.append(skew)
 
-        return (np.array(pos_list), np.array(gc_skew_list))
+        pos_list = np.array(pos_list).astype(np.int64)
+        gc_skew_list = np.array(gc_skew_list).astype(np.float64)
+
+        return pos_list, gc_skew_list
 
     def calc_gc_content(
         self,
         window_size: int | None = None,
         step_size: int | None = None,
         *,
         seq: str | None = None,
-    ) -> tuple[np.ndarray, np.ndarray]:
+    ) -> tuple[NDArray[np.int64], NDArray[np.float64]]:
         """Calculate GC content in sliding window
 
         Parameters
@@ -190,7 +200,7 @@ def calc_gc_content(
 
         Returns
         -------
-        gc_content_result_tuple : tuple[np.ndarray, np.ndarray]
+        gc_content_result_tuple : tuple[NDArray[np.int64], NDArray[np.float64]]
             Position list & GC content list
         """
         pos_list, gc_content_list = [], []
@@ -212,7 +222,10 @@ def calc_gc_content(
             gc_content = SeqUtils.gc_fraction(subseq) * 100
             gc_content_list.append(gc_content)
 
-        return (np.array(pos_list), np.array(gc_content_list))
+        pos_list = np.array(pos_list).astype(np.int64)
+        gc_content_list = np.array(gc_content_list).astype(np.float64)
+
+        return pos_list, gc_content_list
 
     def get_seqid2seq(self) -> dict[str, str]:
         """Get seqid & complete/contig/scaffold genome sequence dict
@@ -236,14 +249,14 @@ def get_seqid2size(self) -> dict[str, int]:
 
     def get_seqid2features(
         self,
-        feature_type: str | None = "CDS",
+        feature_type: str | list[str] | None = "CDS",
         target_strand: int | None = None,
     ) -> dict[str, list[SeqFeature]]:
         """Get seqid & features in target seqid genome dict
 
         Parameters
         ----------
-        feature_type : str | None, optional
+        feature_type : str | list[str] | None, optional
             Feature type (`CDS`, `gene`, `mRNA`, etc...)
             If None, extract regardless of feature type.
         target_strand : int | None, optional
@@ -254,12 +267,15 @@ def get_seqid2features(
         seqid2features : dict[str, list[SeqFeature]]
             seqid & features dict
         """
+        if isinstance(feature_type, str):
+            feature_type = [feature_type]
+
         seqid2features = defaultdict(list)
         for rec in self.records:
             feature: SeqFeature
             for feature in rec.features:
                 strand = feature.location.strand
-                if feature_type is not None and feature.type != feature_type:
+                if feature_type is not None and feature.type not in feature_type:
                     continue
                 if target_strand is not None and strand != target_strand:
                     continue
@@ -279,15 +295,16 @@ def get_seqid2features(
 
     def extract_features(
         self,
-        feature_type: str | None = "CDS",
+        feature_type: str | list[str] | None = "CDS",
+        *,
         target_strand: int | None = None,
         target_range: tuple[int, int] | None = None,
     ) -> list[SeqFeature]:
         """Extract features (only first record)
 
         Parameters
         ----------
-        feature_type : str | None, optional
+        feature_type : str | list[str] | None, optional
             Feature type (`CDS`, `gene`, `mRNA`, etc...)
             If None, extract regardless of feature type.
         target_strand : int | None, optional