iplotx 1.0.0__py3-none-any.whl → 1.1.0__py3-none-any.whl

iplotx/ingest/providers/network/graph_tool.py

@@ -0,0 +1,100 @@
+from typing import (
+    Optional,
+    Sequence,
+)
+from collections.abc import Hashable
+import importlib
+import numpy as np
+import pandas as pd
+
+from ....typing import (
+    LayoutType,
+)
+from ...heuristics import (
+    normalise_layout,
+)
+from ...typing import (
+    NetworkDataProvider,
+    NetworkData,
+)
+from ....utils.internal import (
+    _make_layout_columns,
+)
+
+
+class GraphToolDataProvider(NetworkDataProvider):
+    def __call__(
+        self,
+        layout: Optional[LayoutType] = None,
+        vertex_labels: Optional[Sequence[str] | dict[Hashable, str] | pd.Series] = None,
+        edge_labels: Optional[Sequence[str] | dict[str]] = None,
+    ) -> NetworkData:
+        """Create network data object for iplotx from an igraph object."""
+
+        # Get layout
+        vertex_df = normalise_layout(
+            layout,
+            network=self.network,
+            nvertices=self.number_of_vertices(),
+        )
+        ndim = vertex_df.shape[1]
+        vertex_df.columns = _make_layout_columns(ndim)
+
+        # Vertices are ordered integers, no gaps
+
+        # Vertex labels
+        # Recast vertex_labels=False as vertex_labels=None
+        if np.isscalar(vertex_labels) and (not vertex_labels):
+            vertex_labels = None
+        if vertex_labels is not None:
+            if np.isscalar(vertex_labels):
+                vertex_df["label"] = vertex_df.index.astype(str)
+            elif len(vertex_labels) != len(vertex_df):
+                raise ValueError("Vertex labels must be the same length as the number of vertices.")
+            else:
+                vertex_df["label"] = vertex_labels
+
+        # Edges are a list of tuples, because of multiedges
+        tmp = []
+        for edge in self.network.edges():
+            row = {"_ipx_source": edge.source(), "_ipx_target": edge.target()}
+            # TODO: add graph-tool edge attributes
+            # row.update(edge.attributes())
+            tmp.append(row)
+        if len(tmp):
+            edge_df = pd.DataFrame(tmp)
+        else:
+            edge_df = pd.DataFrame(columns=["_ipx_source", "_ipx_target"])
+        del tmp
+
+        # Edge labels
+        if edge_labels is not None:
+            if len(edge_labels) != len(edge_df):
+                raise ValueError("Edge labels must be the same length as the number of edges.")
+            edge_df["label"] = edge_labels
+
+        network_data = {
+            "vertex_df": vertex_df,
+            "edge_df": edge_df,
+            "directed": self.is_directed(),
+            "ndim": ndim,
+        }
+        return network_data
+
+    @staticmethod
+    def check_dependencies() -> bool:
+        return importlib.util.find_spec("graph_tool") is not None
+
+    @staticmethod
+    def graph_type():
+        import graph_tool.all as gt
+
+        return gt.Graph
+
+    def is_directed(self):
+        """Whether the network is directed."""
+        return self.network.is_directed()
+
+    def number_of_vertices(self):
+        """The number of vertices/nodes in the network."""
+        return self.network.num_vertices()

iplotx/layout.py

@@ -2,7 +2,10 @@
 Layout functions, currently limited to trees.
 """
 
-from typing import Any
+from typing import (
+    Any,
+    Optional,
+)
 from collections.abc import (
     Hashable,
     Callable,
@@ -99,6 +102,8 @@ def _horizontal_tree_layout_right(
 
 def _horizontal_tree_layout(
     orientation="right",
+    start: tuple[float, float] = (0, 0),
+    span: Optional[float] = None,
     **kwargs,
 ) -> dict[Hashable, list[float]]:
     """Horizontal tree layout."""
@@ -110,11 +115,24 @@ def _horizontal_tree_layout(
     if orientation == "left":
         for key in layout:
             layout[key][0] *= -1
+
+    if span is not None:
+        cur_span = len(layout) - 1
+        for key in layout:
+            layout[key][1] = float(layout[key][1]) * span / cur_span
+
+    if start != (0, 0):
+        for key in layout:
+            layout[key][0] += start[0]
+            layout[key][1] += start[1]
+
     return layout
 
 
 def _vertical_tree_layout(
     orientation="descending",
+    start: tuple[float, float] = (0, 0),
+    span: Optional[float] = None,
     **kwargs,
 ) -> dict[Hashable, list[float]]:
     """Vertical tree layout."""
@@ -125,6 +143,17 @@ def _vertical_tree_layout(
         layout[key] = value[::-1]
         # Orient vertically
         layout[key][1] *= sign
+
+    if span is not None:
+        cur_span = len(layout) - 1
+        for key in layout:
+            layout[key][0] = float(layout[key][0]) * span / cur_span
+
+    if start != (0, 0):
+        for key in layout:
+            layout[key][0] += start[0]
+            layout[key][1] += start[1]
+
     return layout
 
 

iplotx/tree/__init__.py

@@ -669,6 +669,7 @@ class TreeArtist(mpl.artist.Artist):
     def scalebar(
         self,
         loc: str = "upper left",
+        label_format: str = ".2f",
         **kwargs,
     ):
         """Create scalebar for the tree.
@@ -689,6 +690,8 @@ class TreeArtist(mpl.artist.Artist):
             self,
             layout=self.get_layout_name(),
             loc=loc,
+            label_format=label_format,
+            **kwargs,
         )
 
         # Remove previous scalebars if any

iplotx/tree/scalebar.py

@@ -37,13 +37,15 @@ class TreeScalebarArtist(Legend):
         self,
         treeartist,
         layout: str = "horizontal",
-        frameon=False,
+        frameon: bool = False,
+        label_format: str = ".2f",
         **kwargs,
     ):
         handles = [treeartist.get_edges()]
         labels = [""]
         self._layout = layout
         self._treeartist = treeartist
+        self._label_format = label_format
 
         if layout == "vertical":
             handler_kwargs = dict(xerr_size=0, yerr_size=1)
@@ -191,13 +193,12 @@ class TreeScalebarArtist(Legend):
 
         bar_trans = bar_handle.get_transform()
         data_trans = self.parent.transData
-        # FIXME: this is off, probably because of some Packer anchor additional transform
         composite_trans = data_trans.inverted() + bar_trans
 
         p0_data = composite_trans.transform(p0)
         p1_data = composite_trans.transform(p1)
         distance = np.linalg.norm(p1_data - p0_data)
-        label = f"{distance:.2f}"
+        label = format(distance, self._label_format)
         return label
 
     def draw(self, renderer):

iplotx/version.py

@@ -2,4 +2,4 @@
 iplotx version information module.
 """
 
-__version__ = "1.0.0"
+__version__ = "1.1.0"

{iplotx-1.0.0.dist-info → iplotx-1.1.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: iplotx
-Version: 1.0.0
+Version: 1.1.0
 Summary: Plot networkx from igraph and networkx.
 Project-URL: Homepage, https://github.com/fabilab/iplotx
 Project-URL: Documentation, https://readthedocs.org/iplotx
@@ -53,14 +53,15 @@ Supports:
 - **networks**:
   - [networkx](https://networkx.org/)
   - [igraph](igraph.readthedocs.io/)
-  - [minimal network data structure](https://iplotx.readthedocs.io/en/latest/gallery/plot_simplenetworkdataprovider.html#sphx-glr-gallery-plot-simplenetworkdataprovider-py) (zero dependency)
+  - [graph-tool](https://graph-tool.skewed.de/)
+  - [zero-dependency](https://iplotx.readthedocs.io/en/latest/gallery/plot_simplenetworkdataprovider.html#sphx-glr-gallery-plot-simplenetworkdataprovider-py)
 - **trees**:
   - [ETE4](https://etetoolkit.github.io/ete/)
   - [cogent3](https://cogent3.org/)
   - [Biopython](https://biopython.org/)
   - [scikit-bio](https://scikit.bio)
   - [dendropy](https://jeetsukumaran.github.io/DendroPy/index.html)
-  - [minimal tree data structure](https://iplotx.readthedocs.io/en/latest/gallery/tree/plot_simpletreedataprovider.html#sphx-glr-gallery-tree-plot-simpletreedataprovider-py) (zero dependency)
+  - [zero-dependency](https://iplotx.readthedocs.io/en/latest/gallery/tree/plot_simpletreedataprovider.html#sphx-glr-gallery-tree-plot-simpletreedataprovider-py)
 
 In addition to the above, *any* network or tree analysis library can register an [entry point](https://iplotx.readthedocs.io/en/latest/providers.html#creating-a-custom-data-provider) to gain compatibility with `iplotx` with no intervention from our side.
 
@@ -81,7 +82,7 @@ fig, ax = plt.subplots(figsize=(3, 3))
 ipx.plot(g, ax=ax, layout=layout)
 ```
 
-![Quick start image](docs/source/_static/graph_basic.png)
+![Quick start image](/docs/source/_static/graph_basic.png)
 
 ## Documentation
 See [readthedocs](https://iplotx.readthedocs.io/en/latest/) for the full documentation.
@@ -90,11 +91,11 @@ See [readthedocs](https://iplotx.readthedocs.io/en/latest/) for the full documen
 See [gallery](https://iplotx.readthedocs.io/en/latest/gallery/index.html).
 
 ## Features
-- Plot networks from multiple libraries including networkx and igraph, using matplotlib as a backend. ✅
+- Plot networks from multiple libraries including networkx, igraph and graph-tool, using Matplotlib. ✅
 - Plot trees from multiple libraries such as cogent3, ETE4, skbio, biopython, and dendropy. ✅
 - Flexible yet easy styling, including an internal library of styles ✅
 - Interactive plotting, e.g. zooming and panning after the plot is created. ✅
-- Store the plot to disk thanks to the many matplotlib backends (SVG, PNG, PDF, etc.). ✅
+- Store the plot to disk in many formats (SVG, PNG, PDF, GIF, etc.). ✅
 - 3D network visualisation with depth shading. ✅
 - Efficient plotting of large graphs (up to ~1 million nodes on a laptop). ✅
 - Edit plotting elements after the plot is created, e.g. changing node colors, labels, etc. ✅

{iplotx-1.0.0.dist-info → iplotx-1.1.0.dist-info}/RECORD

@@ -1,10 +1,10 @@
 iplotx/__init__.py,sha256=RzSct91jO8abrxOIn33rKEnDUgYpu1oj4olbObgX_hs,489
 iplotx/artists.py,sha256=2dBDT240zGwKb6tIc_y9pXeyU3LuYeF9wjj2tvi4KJo,730
 iplotx/label.py,sha256=7eS8ByadrhdIFOZz19U4VrS-oXY_ndFYNB-D4RZbFqI,9573
-iplotx/layout.py,sha256=KxmRLqjo8AYCBAmXez8rIiLU2sM34qhb6ox9AHYwRyE,4839
+iplotx/layout.py,sha256=S-iFxHaIOzhBDG2JUzl9_oDBRP5TYY1hXnEOs0h1Rck,5588
 iplotx/plotting.py,sha256=FvV33DCuEjJwO9ytiYJuQmfOywgF-cDANd6nEE5s8R0,13211
 iplotx/typing.py,sha256=QLdzV358IiD1CFe88MVp0D77FSx5sSAVUmM_2WPPE8I,1463
-iplotx/version.py,sha256=Zw6LAvjlzbItG1QBPJb1Tuqkb2PVUYsDwCVRYEJusgc,66
+iplotx/version.py,sha256=mrnbNTnvhHXH5H10Drqi5HLqPXOwoyNlRYIAv7vTAy0,66
 iplotx/vertex.py,sha256=_yYyvusn4vYvi6RBEW6CHa3vnbv43GnZylnMIaK4bG0,16040
 iplotx/art3d/vertex.py,sha256=Xf8Um30X2doCd8KdNN7332F6BxC4k72Mb_GeRAuzQfQ,2545
 iplotx/art3d/edge/__init__.py,sha256=uw1U_mMXqcZAvea-7JbU1PUKULQD1CMMrbwY02tiWRQ,8529
@@ -18,6 +18,7 @@ iplotx/edge/ports.py,sha256=BpkbiEhX4mPBBAhOv4jcKFG4Y8hxXz5GRtVLCC0jbtI,1235
 iplotx/ingest/__init__.py,sha256=S0YfnXcFKseB7ZBQc4yRt0cNDsLlhqdom0TmSY3OY2E,4756
 iplotx/ingest/heuristics.py,sha256=715VqgfKek5LOJnu1vTo7RqPgCl-Bb8Cf6o7_Tt57fA,5797
 iplotx/ingest/typing.py,sha256=61LwNwrTHVh8eqqC778Gr81zPYcUKW61mDgGCCsuGSk,14181
+iplotx/ingest/providers/network/graph_tool.py,sha256=iTCf4zHe4Zmdd8Tlz6j7Xfo_FwfsIiK5JkQfH3uq7TM,3028
 iplotx/ingest/providers/network/igraph.py,sha256=WL9Yx2IF5QhUIoKMlozdyq5HWIZ-IJmNoeS8GOhL0KU,2945
 iplotx/ingest/providers/network/networkx.py,sha256=ehCg4npL073HX-eAG-VoP6refLPsMb3lYG51xt_rNjA,4636
 iplotx/ingest/providers/network/simple.py,sha256=e_aHhiHhN9DrMoNrt7tEMPURXGhQ1TYRPzsxDEptUlc,3766
@@ -32,13 +33,13 @@ iplotx/network/groups.py,sha256=E_eYVXRHjv1DcyA4RupTkMa-rRFrIKkt9Rxn_Elw9Nc,6796
 iplotx/style/__init__.py,sha256=rf1GutrE8hHUhCoe4FGKYX-aNtHuu_U-kYQnqUxZNrY,10282
 iplotx/style/leaf_info.py,sha256=3xBn7xv9Uy2KAqdhM9S6ew5ZBJrGRTXRL3xXb8atfLw,1018
 iplotx/style/library.py,sha256=58Y8BlllGLsR4pQM7_PVCP5tH6_4GkchXZvJpqGHlcg,8534
-iplotx/tree/__init__.py,sha256=6a8cbTd-OS-x8GEZJeRo3vneVjI98AiQW_gIo1H7h3Y,29969
+iplotx/tree/__init__.py,sha256=mFCgXSusB1dSMc-xN_zOc5PojpEf_XyP8yR3xeZVQMY,30065
 iplotx/tree/cascades.py,sha256=on5GyqbWasl1zgK7bYXYQE0LOSfHc1z-1hnm0GWd6aw,8184
-iplotx/tree/scalebar.py,sha256=QC2l-Nx39g8fkO1tHHvbrtzLncfQc9L57BQniSk2h5Q,11849
+iplotx/tree/scalebar.py,sha256=Yxt_kF8JdTwKGa8Jzqt3qVePPK5ZBG8P0EiONrsh3E8,11863
 iplotx/utils/geometry.py,sha256=6RrC6qaB0-1vIk1LhGA4CfsiMd-9JNniSPyL_l9mshE,9245
 iplotx/utils/internal.py,sha256=WWfcZDGK8Ut1y_tOHRGg9wSqY1bwSeLQO7dHM_8Tvwo,107
 iplotx/utils/matplotlib.py,sha256=p_53Oamof0RI4mtV8HrdDtZbgVqUxeUZ_KDvLZSiBUQ,8604
 iplotx/utils/style.py,sha256=vyNP80nDYVinqm6_9ltCJCtjK35ZcGlHvOskNv3eQBc,4225
-iplotx-1.0.0.dist-info/METADATA,sha256=VsUs2_FiPrGNcfAfnL-T0fB9RObJCdAUvjaEUO46vFg,5086
-iplotx-1.0.0.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
-iplotx-1.0.0.dist-info/RECORD,,
+iplotx-1.1.0.dist-info/METADATA,sha256=BBWbFLjqgs00VaB3DXNSex39oA0iDplDgBeCmrO6hKw,5053
+iplotx-1.1.0.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
+iplotx-1.1.0.dist-info/RECORD,,