Merge pull request #57 from moshi4/develop

Bump to v1.3.0

.github/workflows/ci.yml

@@ -17,10 +17,10 @@ jobs:
         python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
     steps:
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Setup Python ${{ matrix.python-version}}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
 

.github/workflows/publish_mkdocs.yml

@@ -10,10 +10,10 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Setup Python 3.11
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: "3.11"
 

.github/workflows/publish_to_pypi.yml

@@ -13,10 +13,10 @@ jobs:
       PYPI_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
     steps:
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Setup Python 3.11
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: "3.11"
 

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "pyCirclize"
-version = "1.2.0"
+version = "1.3.0"
 description = "Circular visualization in Python"
 authors = ["moshi4"]
 license = "MIT"

src/pycirclize/__init__.py

@@ -1,6 +1,6 @@
 from pycirclize.circos import Circos
 
-__version__ = "1.2.0"
+__version__ = "1.3.0"
 
 __all__ = [
     "Circos",

src/pycirclize/config.py

@@ -12,7 +12,7 @@
 MIN_R = 0
 MAX_R = 100
 R_PLOT_MARGIN = 5
-ARC_RADIAN_STEP = 0.001
+ARC_RADIAN_STEP = 0.01
 R_LIM = (MIN_R, MAX_R)
 AXIS_FACE_PARAM = dict(zorder=0.99, ec="none", edgecolor="none")
 AXIS_EDGE_PARAM = dict(zorder=1.01, fc="none", facecolor="none")

src/pycirclize/parser/matrix.py

@@ -102,10 +102,11 @@ def parse_fromto_table(
         fromto2value = defaultdict(int)
         for row in fromto_table.itertuples():
             from_label, to_label, value = str(row[1]), str(row[2]), row[3]
-            fromto = f"{from_label}{to_label}"
-            fromto2value[fromto] = value
-            label2value_sum[from_label] += value
-            label2value_sum[to_label] += value
+            if float(value) > 0:
+                fromto = f"{from_label}{to_label}"
+                fromto2value[fromto] = value
+                label2value_sum[from_label] += value
+                label2value_sum[to_label] += value
         all_labels = list(label2value_sum.keys())
 
         # Set user specified label order

src/pycirclize/track.py

@@ -1321,7 +1321,8 @@ def _to_arc_radr(
                 all_arc_rad.extend([rad1, rad2])
                 all_arc_r.extend([r1, r2])
             else:
-                step = config.ARC_RADIAN_STEP
+                # To obtain finely chopped coordinates, step is reduced by a tenth
+                step = config.ARC_RADIAN_STEP / 10
                 if rad1 > rad2:
                     step *= -1
                 arc_rad = list(np.arange(rad1, rad2, step)) + [rad2]

src/pycirclize/tree.py

@@ -246,6 +246,49 @@ def get_target_xlim(
         )
         return target_xlim
 
+    def show_confidence(
+        self,
+        *,
+        size: float = 8,
+        orientation: str = "vertical",
+        label_formatter: Callable[[float], str] | None = None,
+        **kwargs,
+    ) -> None:
+        """Show confidence value on each internal node of the phylogenetic tree
+
+        Parameters
+        ----------
+        size : float, optional
+            Text size
+        orientation : str, optional
+            Text orientation (`horizontal` or `vertical`)
+        label_formatter : Callable[[float], str] | None, optional
+            User-defined function for label format.
+        **kwargs : dict, optional
+            Text properties (e.g. `color="red", ...`)
+            <https://matplotlib.org/stable/api/_as_gen/matplotlib.axes.Axes.text.html>
+        """
+        node: Clade
+        for node in self.tree.get_nonterminals():
+            # Ignore if confidence value is None
+            confidence = node.confidence
+            if confidence is None:
+                continue
+
+            # Format confidence label
+            if label_formatter:
+                label = label_formatter(float(confidence))
+            elif str(confidence).isdigit():
+                label = str(confidence)
+            else:
+                label = f"{float(confidence):.2f}"
+
+            # Get target node x, r coordinate
+            x, r = self.name2xr[str(node.name)]
+
+            kwargs.update(size=size, orientation=orientation)
+            self.track.parent_sector.text(label, x, r + 1.0, **kwargs)
+
     def highlight(
         self,
         query: str | list[str] | tuple[str],

src/pycirclize/utils/example_data/trees/alphabet.nwk

@@ -1 +1 @@
-(((A:1.90623,(B:0.77315,(C:0.78332,(D:2.24573,(E:1.25976,F:1.85780):0.00000):0.15046):1.04012):0.90160):0.72056,((((G:0.59616,H:1.70149):1.58325,I:1.00419):1.19115,(J:0.91877,K:1.31367):0.88856):1.55681,L:0.88143):0.74292):1.02610,((M:1.46117,((N:0.12272,(O:1.12953,P:0.58300):0.73047):0.70152,(Q:0.71106,((((R:0.53759,S:0.71617):1.49010,T:1.40058):1.09120,(U:0.80607,V:1.06576):0.73818):0.94044,W:1.90216):1.65416):1.75184):0.90540):1.56327,(X:0.59332,(Y:1.23427,Z:1.60350):0.98802):0.87582):0.47830):0.00000;
+(((A:1.90623,(B:0.77315,(C:0.78332,(D:2.24573,(E:1.25976,F:1.85780)95:0.00000)99:0.15046)99:1.04012)100:0.90160)99:0.72056,((((G:0.59616,H:1.70149)91:1.58325,I:1.00419)98:1.19115,(J:0.91877,K:1.31367)91:0.88856)99:1.55681,L:0.88143)99:0.74292)95:1.02610,((M:1.46117,((N:0.12272,(O:1.12953,P:0.58300)99:0.73047)91:0.70152,(Q:0.71106,((((R:0.53759,S:0.71617)90:1.49010,T:1.40058)100:1.09120,(U:0.80607,V:1.06576)99:0.73818)100:0.94044,W:1.90216)91:1.65416)93:1.75184)90:0.90540)91:1.56327,(X:0.59332,(Y:1.23427,Z:1.60350)93:0.98802)90:0.87582)97:0.47830)100:0.00000;

tests/test_plot.py

@@ -182,6 +182,8 @@ def test_phylogenetic_tree_plot(fig_outfile: Path):
     tv.set_node_line_props(["S", "R"], color="lime", descendent=False)
     tv.set_node_line_props(["X", "Y", "Z"], color="purple", apply_label_color=True)
 
+    tv.show_confidence()
+
     circos.savefig(fig_outfile)
     assert fig_outfile.exists()