iplotx 0.2.0__py3-none-any.whl → 0.3.0__py3-none-any.whl

iplotx/vertex.py

@@ -6,7 +6,6 @@ from typing import (
     Optional,
     Sequence,
     Any,
-    Never,
 )
 import warnings
 import numpy as np
@@ -70,20 +69,21 @@ class VertexCollection(PatchCollection):
         self._index = layout.index
         self._style = style
         self._labels = labels
+        self._layout = layout
+        self._layout_coordinate_system = layout_coordinate_system
 
         # Create patches from structured data
-        patches, offsets, sizes, kwargs2 = self._init_vertex_patches(
-            layout,
-            layout_coordinate_system=layout_coordinate_system,
-        )
+        patches, sizes, kwargs2 = self._init_vertex_patches()
 
         kwargs.update(kwargs2)
-        kwargs["offsets"] = offsets
         kwargs["match_original"] = True
 
         # Pass to PatchCollection constructor
         super().__init__(patches, *args, **kwargs)
 
+        # Set offsets in coordinate system
+        self._update_offsets_from_layout()
+
         # Compute _transforms like in _CollectionWithScales for dpi issues
         self.set_sizes(sizes)
 
@@ -100,10 +100,11 @@ class VertexCollection(PatchCollection):
             children.append(self._label_collection)
         return tuple(children)
 
-    def set_figure(self, fig) -> Never:
+    def set_figure(self, fig) -> None:
         """Set the figure for this artist and all children."""
         super().set_figure(fig)
         self.set_sizes(self._sizes, self.get_figure(root=True).dpi)
+        self._update_children()
         for child in self.get_children():
             child.set_figure(fig)
 
@@ -123,7 +124,7 @@ class VertexCollection(PatchCollection):
         """Get vertex sizes (max of width and height), scaled by dpi."""
         return self._transforms[:, 0, 0]
 
-    def set_sizes(self, sizes, dpi=72.0):
+    def set_sizes(self, sizes, dpi: float = 72.0) -> None:
         """Set vertex sizes.
 
         This rescales the current vertex symbol/path linearly, using this
@@ -146,9 +147,74 @@ class VertexCollection(PatchCollection):
     get_size = get_sizes
     set_size = set_sizes
 
-    def _init_vertex_patches(
-        self, vertex_layout_df, layout_coordinate_system="cartesian"
-    ):
+    def get_layout(self) -> pd.DataFrame:
+        """Get the vertex layout.
+
+        Returns:
+            The vertex layout as a DataFrame.
+        """
+        return self._layout
+
+    def get_layout_coordinate_system(self) -> str:
+        """Get the layout coordinate system.
+
+        Returns:
+            Name of the layout coordinate system, e.g. "cartesian" or "polar".
+        """
+        return self._layout_coordinate_system
+
+    def get_offsets(self, ignore_layout: bool = True) -> np.ndarray:
+        """Get the vertex offsets.
+
+        Parameters:
+            ignore_layout: If True, return the matplotlib Artist._offsets directly, ignoring the
+                layout coordinate system. If False, it's equivalent to get_layout().values.
+
+        Returns:
+            The vertex offsets as a 2D numpy array.
+
+        Note: It is best for users to *not* ignore the layout coordinate system, as it may lead
+        to inconsistencies. However, some internal matplotlib functions require the default
+        signature of this function to look at the vanilla offsets, hence the default parameters.
+        """
+        if not ignore_layout:
+            return self.get_layout().values
+        else:
+            return self._offsets
+
+    def _update_offsets_from_layout(self) -> None:
+        """Update offsets in matplotlib coordinates from the layout DataFrame."""
+        if self._layout_coordinate_system == "cartesian":
+            self._offsets = self._layout.values
+        elif self._layout_coordinate_system == "polar":
+            # Convert polar coordinates (r, theta) to cartesian (x, y)
+            r = self._layout.iloc[:, 0].values
+            theta = self._layout.iloc[:, 1].values
+            if self._offsets is None:
+                self._offsets = np.zeros((len(r), 2))
+            self._offsets[:, 0] = r * np.cos(theta)
+            self._offsets[:, 1] = r * np.sin(theta)
+        else:
+            raise ValueError(
+                f"Layout coordinate system not supported: {self._layout_coordinate_system}."
+            )
+
+    def set_offsets(self, offsets: np.ndarray) -> None:
+        """Set the vertex positions/offsets in layout coordinates.
+
+        Parameters:
+            offsets: Array of coordinates in the layout coordinate system. For polar layouts,
+                these should be in the form of (r, theta) pairs.
+        """
+        self._layout.values[:] = offsets
+        self._update_offsets_from_layout()
+        self.stale = True
+
+    def get_style(self) -> Optional[dict[str, Any]]:
+        """Get the style dictionary for the vertices."""
+        return self._style
+
+    def _init_vertex_patches(self):
         style = self._style or {}
         if "cmap" in style:
             cmap_fun = _build_cmap_fun(
@@ -164,32 +230,17 @@ class VertexCollection(PatchCollection):
                     "No labels found, cannot resize vertices based on labels."
                 )
                 style["size"] = get_style("default.vertex")["size"]
-            else:
-                vertex_labels = self._labels
 
         if "cmap" in style:
             colorarray = []
         patches = []
-        offsets = []
         sizes = []
-        for i, (vid, row) in enumerate(vertex_layout_df.iterrows()):
-            # Centre of the vertex
-            offset = list(row.values)
-
-            # Transform to cartesian coordinates if needed
-            if layout_coordinate_system == "polar":
-                r, theta = offset
-                offset = [r * np.cos(theta), r * np.sin(theta)]
-
-            offsets.append(offset)
-
-            if style.get("size") == "label":
-                # NOTE: it's ok to overwrite the dict here
-                style["size"] = _get_label_width_height(
-                    str(vertex_labels[vid]), **style.get("label", {})
-                )
-
+        for i, (vid, row) in enumerate(self._layout.iterrows()):
             stylei = rotate_style(style, index=i, key=vid)
+            if stylei.get("size", 20) == "label":
+                stylei["size"] = _get_label_width_height(
+                    str(self._labels[vid]), **style.get("label", {})
+                )
             if cmap_fun is not None:
                 colorarray.append(style["facecolor"])
                 stylei["facecolor"] = cmap_fun(stylei["facecolor"])
@@ -207,7 +258,7 @@ class VertexCollection(PatchCollection):
             kwargs["cmap"] = style["cmap"]
             kwargs["norm"] = norm
 
-        return patches, offsets, sizes, kwargs
+        return patches, sizes, kwargs
 
     def _compute_label_collection(self):
         transform = self.get_offset_transform()
@@ -230,6 +281,12 @@ class VertexCollection(PatchCollection):
         )
 
     def get_labels(self):
+        """Get the vertex labels.
+
+        Returns:
+            The artist with the LabelCollection.
+        """
+
         if hasattr(self, "_label_collection"):
             return self._label_collection
         else:
@@ -245,6 +302,30 @@ class VertexCollection(PatchCollection):
         if val and hasattr(self, "stale_callback_post"):
             self.stale_callback_post(self)
 
+    def _update_children(self) -> None:
+        """Update children before drawing and before first render."""
+        self._update_labels()
+
+    def _update_labels(self) -> None:
+        """Update labels before drawing.
+
+        NOTE: This needs to work in figure coordinates.
+        """
+        if not hasattr(self, "_label_collection"):
+            return
+
+        if self.get_layout_coordinate_system() != "polar":
+            return
+
+        transform = self.get_offset_transform()
+        trans = transform.transform
+
+        zero_fig = trans(np.array([0, 0]))
+        offsets_fig = trans(self.get_labels().get_offsets())
+        doffsets_fig = offsets_fig - zero_fig
+        rotations = np.arctan2(doffsets_fig[:, 1], doffsets_fig[:, 0])
+        self.get_labels().set_rotations(rotations)
+
     @mpl.artist.allow_rasterization
     def draw(self, renderer):
         if not self.get_visible():
@@ -257,6 +338,9 @@ class VertexCollection(PatchCollection):
 
         self.set_sizes(self._sizes, self.get_figure(root=True).dpi)
 
+        # Set the label rotations already, hopefully this is not too early
+        self._update_children()
+
         # NOTE: This draws the vertices first, then the labels.
         # The correct order would be vertex1->label1->vertex2->label2, etc.
         # We might fix if we manage to find a way to do it.
@@ -266,10 +350,12 @@ class VertexCollection(PatchCollection):
 
 
 def make_patch(
-    marker: str, size: float | Sequence[float], **kwargs
+    marker: str = "o",
+    size: float | Sequence[float] = 20,
+    **kwargs,
 ) -> tuple[Patch, float]:
     """Make a patch of the given marker shape and size."""
-    forbidden_props = ["label", "cmap", "norm"]
+    forbidden_props = ["label", "cmap", "norm", "cascade"]
     for prop in forbidden_props:
         if prop in kwargs:
             kwargs.pop(prop)
@@ -280,7 +366,8 @@ def make_patch(
 
     # Size of vertices is determined in self._transforms, which scales with dpi, rather than here,
     # so normalise by the average dimension (btw x and y) to keep the ratio of the marker.
-    # If you check in get_sizes, you will see that rescaling also happens with the max of width and height.
+    # If you check in get_sizes, you will see that rescaling also happens with the max of width
+    # and height.
     size = np.asarray(size, dtype=float)
     size_max = size.max()
     if size_max > 0:

{iplotx-0.2.0.dist-info → iplotx-0.3.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: iplotx
-Version: 0.2.0
+Version: 0.3.0
 Summary: Plot networkx from igraph and networkx.
 Project-URL: Homepage, https://github.com/fabilab/iplotx
 Project-URL: Documentation, https://readthedocs.org/iplotx
@@ -11,12 +11,20 @@ Author-email: Fabio Zanini <fabio.zanini@unsw.edu.au>
 Maintainer-email: Fabio Zanini <fabio.zanini@unsw.edu.au>
 License: MIT
 Keywords: graph,network,plotting,visualisation
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Developers
+Classifier: Intended Audience :: Education
+Classifier: Intended Audience :: Science/Research
 Classifier: License :: OSI Approved :: MIT License
+Classifier: Natural Language :: English
 Classifier: Operating System :: OS Independent
 Classifier: Programming Language :: Python :: 3
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Classifier: Programming Language :: Python :: 3.13
+Classifier: Topic :: Scientific/Engineering :: Visualization
+Classifier: Topic :: System :: Networking
+Classifier: Typing :: Typed
 Requires-Python: >=3.11
 Requires-Dist: matplotlib>=2.0.0
 Requires-Dist: numpy>=2.0.0
@@ -31,11 +39,12 @@ Description-Content-Type: text/markdown
 ![Github Actions](https://github.com/fabilab/iplotx/actions/workflows/test.yml/badge.svg)
 ![PyPI - Version](https://img.shields.io/pypi/v/iplotx)
 ![RTD](https://readthedocs.org/projects/iplotx/badge/?version=latest)
+![pylint](assets/pylint.svg)
 
 # iplotx
 Plotting networks from igraph and networkx.
 
-**NOTE**: This is currently alpha quality software. The API and functionality will break constantly, so use at your own risk. That said, if you have things you would like to see improved, please open a GitHub issue.
+**NOTE**: This is currently beta quality software. The API and functionality are settling in and might break occasionally.
 
 ## Installation
 ```bash
@@ -68,9 +77,13 @@ See [gallery](https://iplotx.readthedocs.io/en/latest/gallery/index.html).
 - Support storing the plot to disk thanks to the many matplotlib backends (SVG, PNG, PDF, etc.). ✅
 - Support flexible yet easy styling. ✅
 - Efficient plotting of large graphs using matplotlib's collection functionality. ✅
+- Support editing plotting elements after the plot is created, e.g. changing node colors, labels, etc. ✅
+- Support animations, e.g. showing the evolution of a network over time. ✅
+- Support mouse interaction, e.g. hovering over or clicking on nodes and edges to get information about them. ✅
 - Support trees from special libraries such as ete3, biopython, etc. This will need a dedicated function and layouting. ✅
-- Support animations, e.g. showing the evolution of a network over time. 🏗️
 - Support uni- and bi-directional communication between graph object and plot object.🏗️
 
+**NOTE:** The last item can probably be achieved already by using `matplotlib`'s existing callback functionality. It is currently untested, but if you manage to get it to work on your graph let me know and I'll add it to the examples (with credit).
+
 ## Authors
 Fabio Zanini (https://fabilab.org)

iplotx-0.3.0.dist-info/RECORD

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iplotx-0.2.0.dist-info/RECORD

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