iplotx 0.6.5__py3-none-any.whl → 0.6.7__py3-none-any.whl

iplotx/edge/__init__.py

@@ -131,6 +131,9 @@ class EdgeCollection(mpl.collections.PatchCollection):
                 self._style["split"],
             )
 
+        zorder = self._style.get("zorder", 2)
+        self.set_zorder(zorder)
+
     def _add_subedges(
         self,
         nedges,

iplotx/ingest/providers/network/networkx.py

@@ -101,7 +101,13 @@ class NetworkXDataProvider(NetworkDataProvider):
             else:
                 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
+                if isinstance(edge_labels, dict):
+                    edge_labels = pd.Series(edge_labels)
+                    edge_df["label"] = edge_labels.loc[
+                        edge_df.set_index(["_ipx_source", "_ipx_target"]).index
+                    ].values
+                else:
+                    edge_df["label"] = edge_labels
 
         network_data = {
             "vertex_df": vertex_df,

iplotx/ingest/typing.py

@@ -138,11 +138,13 @@ class TreeDataProvider(Protocol):
 
         Note: This is a default implemntation that can be overridden by the provider.
         """
-        root_attr = self.tree.root
-        if callable(root_attr):
-            return root_attr()
-        else:
-            return root_attr
+        if hasattr(self.tree, "root"):
+            root_attr = self.tree.root
+            if callable(root_attr):
+                return root_attr()
+            else:
+                return root_attr
+        return self.tree.get_root()
 
     def get_leaves(self) -> Sequence[Any]:
         """Get the tree leaves/tips in a provider-specific data structure.

iplotx/network.py

@@ -140,7 +140,10 @@ class NetworkArtist(mpl.artist.Artist):
         return self
 
     def get_children(self):
-        return (self._vertices, self._edges)
+        if hasattr(self, "_edges"):
+            return (self._vertices, self._edges)
+        else:
+            return (self._vertices,)
 
     def set_figure(self, fig):
         super().set_figure(fig)
@@ -184,12 +187,14 @@ class NetworkArtist(mpl.artist.Artist):
         if len(layout) == 0:
             return mpl.transforms.Bbox([[0, 0], [1, 1]])
 
-        bbox = mpl.transforms.Bbox.union(
-            [
-                self._vertices.get_datalim(transData),
+        bboxes = [
+            self._vertices.get_datalim(transData),
+        ]
+        if hasattr(self, "_edges"):
+            bboxes.append(
                 self._edges.get_datalim(transData),
-            ]
-        )
+            )
+        bbox = mpl.transforms.Bbox.union(bboxes)
 
         bbox = bbox.expanded(sw=(1.0 + pad), sh=(1.0 + pad))
         return bbox
@@ -241,6 +246,9 @@ class NetworkArtist(mpl.artist.Artist):
 
         edge_df = self._ipx_internal_data["edge_df"].set_index(["_ipx_source", "_ipx_target"])
 
+        if len(edge_df) == 0:
+            return
+
         if "cmap" in edge_style:
             cmap_fun = _build_cmap_fun(
                 edge_style,
@@ -313,8 +321,7 @@ class NetworkArtist(mpl.artist.Artist):
         if not self.get_visible():
             return
 
-        # NOTE: looks like we have to manage the zorder ourselves
-        # this is kind of funny actually
+        # Handle zorder manually, just like in AxesBase in mpl
         children = list(self.get_children())
         children.sort(key=lambda x: x.zorder)
         for art in children:

iplotx/plotting.py

@@ -28,6 +28,8 @@ def network(
     title: Optional[str] = None,
     aspect: Optional[str | float] = None,
     margins: float | tuple[float, float] = 0,
+    strip_axes: bool = True,
+    figsize: Optional[tuple[float, float]] = None,
     **kwargs,
 ) -> list[mpl.artist.Artist]:
     """Plot this network and/or vertex grouping using the specified layout.
@@ -53,6 +55,10 @@ def network(
             used as a quick fix when some vertex shapes reach beyond the plot edge. This is
             a fraction of the data limits, so 0.1 means 10% of the data limits will be left
             as margin.
+        strip_axes: If True, remove axis spines and ticks.
+        figsize: If ax is None, a new matplotlib Figure is created. This argument specifies
+            the (width, height) dimension of the figure in inches. If ax is not None, this
+            argument is ignored. If None, the default matplotlib figure size is used.
         kwargs: Additional arguments are treated as an alternate way to specify style. If
             both "style" and additional **kwargs are provided, they are both applied in that
             order (style, then **kwargs).
@@ -69,7 +75,7 @@ def network(
             raise ValueError("At least one of network or grouping must be provided.")
 
         if ax is None:
-            fig, ax = plt.subplots()
+            fig, ax = plt.subplots(figsize=figsize)
 
         artists = []
         if network is not None:
@@ -110,7 +116,7 @@ def network(
         if aspect is not None:
             ax.set_aspect(aspect)
 
-        _postprocess_axis(ax, artists)
+        _postprocess_axes(ax, artists, strip=strip_axes)
 
         if np.isscalar(margins):
             margins = (margins, margins)
@@ -132,6 +138,8 @@ def tree(
     title: Optional[str] = None,
     aspect: Optional[str | float] = None,
     margins: float | tuple[float, float] = 0,
+    strip_axes: bool = True,
+    figsize: Optional[tuple[float, float]] = None,
     **kwargs,
 ) -> TreeArtist:
     """Plot a tree using the specified layout.
@@ -140,9 +148,37 @@ def tree(
         tree: The tree to plot. Can be a BioPython.Phylo.Tree object.
         layout: The layout to use for plotting.
         directed: If False, do not draw arrows.
+        vertex_labels: The labels for the vertices. If None or False, no vertex labels. Also
+            read leaf_labels for leaf nodes.
+        leaf_labels: The labels for the leaf nodes. If None or False, no leaf labels are used
+            except if vertex_labels are specified for leaf nodes. This argument and the
+            previous vertex_labels provide somewhat redundant functionality but have quite
+            different default behaviours for distinct use cases. This argument is typically
+            useful for labels that are specific to leaf nodes only (e.g. species in a
+            phylogenetic tree), whereas vertex_labels is typically used for labels that apply
+            to internal nodes too (e.g. branch support values). This redundancy is left on
+            purpose to allow for maximal style flexibility.
         show_support: If True, show the support values for the nodes (assumed to be from 0 to 100,
             rounded to nearest integer). If both this parameter and vertex_labels are set,
             show_support takes precedence and hides the vertex labels.
+        ax: The axis to plot on. If None, a new figure and axis will be created. Defaults to
+            None.
+        style: Apply this style for the objects to plot. This can be a sequence (e.g. list)
+            of styles and they will be applied in order.
+        title: If not None, set the axes title to this value.
+        aspect: If not None, set the aspect ratio of the axis to this value. The most common
+            value is 1.0, which proportionates x- and y-axes.
+        margins: How much margin to leave around the plot. A higher value (e.g. 0.1) can be
+            used as a quick fix when some vertex shapes reach beyond the plot edge. This is
+            a fraction of the data limits, so 0.1 means 10% of the data limits will be left
+            as margin.
+        strip_axes: If True, remove axis spines and ticks.
+        figsize: If ax is None, a new matplotlib Figure is created. This argument specifies
+            the (width, height) dimension of the figure in inches. If ax is not None, this
+            argument is ignored. If None, the default matplotlib figure size is used.
+        kwargs: Additional arguments are treated as an alternate way to specify style. If
+            both "style" and additional **kwargs are provided, they are both applied in that
+            order (style, then **kwargs).
 
     Returns:
         A TreeArtist object, set as a direct child of the matplotlib Axes.
@@ -151,7 +187,7 @@ def tree(
 
     with stylecontext:
         if ax is None:
-            fig, ax = plt.subplots()
+            fig, ax = plt.subplots(figsize=figsize)
 
         artist = TreeArtist(
             tree=tree,
@@ -173,7 +209,7 @@ def tree(
         if aspect is not None:
             ax.set_aspect(aspect)
 
-        _postprocess_axis(ax, [artist])
+        _postprocess_axes(ax, [artist], strip=strip_axes)
 
         if np.isscalar(margins):
             margins = (margins, margins)
@@ -184,18 +220,19 @@ def tree(
 
 
 # INTERNAL ROUTINES
-def _postprocess_axis(ax, artists):
+def _postprocess_axes(ax, artists, strip=True):
     """Postprocess axis after plotting."""
 
-    # Despine
-    ax.spines["right"].set_visible(False)
-    ax.spines["top"].set_visible(False)
-    ax.spines["left"].set_visible(False)
-    ax.spines["bottom"].set_visible(False)
+    if strip:
+        # Despine
+        ax.spines["right"].set_visible(False)
+        ax.spines["top"].set_visible(False)
+        ax.spines["left"].set_visible(False)
+        ax.spines["bottom"].set_visible(False)
 
-    # Remove axis ticks
-    ax.set_xticks([])
-    ax.set_yticks([])
+        # Remove axis ticks
+        ax.set_xticks([])
+        ax.set_yticks([])
 
     # Set new data limits
     bboxes = []

iplotx/version.py

@@ -2,4 +2,4 @@
 iplotx version information module.
 """
 
-__version__ = "0.6.5"
+__version__ = "0.6.7"

iplotx/vertex.py

@@ -68,7 +68,7 @@ class VertexCollection(PatchCollection):
         """
 
         self._index = layout.index
-        self._style = style
+        self._style = style if style is not None else {}
         self._layout = layout
         self._layout_coordinate_system = layout_coordinate_system
 
@@ -94,6 +94,9 @@ class VertexCollection(PatchCollection):
         if self._labels is not None:
             self._compute_label_collection()
 
+        zorder = self._style.get("zorder", 1)
+        self.set_zorder(zorder)
+
     def __len__(self):
         """Return the number of vertices in the collection."""
         return len(self.get_paths())

{iplotx-0.6.5.dist-info → iplotx-0.6.7.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: iplotx
-Version: 0.6.5
+Version: 0.6.7
 Summary: Plot networkx from igraph and networkx.
 Project-URL: Homepage, https://github.com/fabilab/iplotx
 Project-URL: Documentation, https://readthedocs.org/iplotx

{iplotx-0.6.5.dist-info → iplotx-0.6.7.dist-info}/RECORD

@@ -4,22 +4,22 @@ iplotx/cascades.py,sha256=OPqF7Huls-HFmDA5MCF6DEZlUeRVaXsbQcHBoKAgNJs,8182
 iplotx/groups.py,sha256=_9KdIiTAi1kXtd2mDywgBJCbqoRq2z-5fzOPf76Wgb8,6287
 iplotx/label.py,sha256=6am3a0ejcW_bWEXSOODE1Ke3AyCU1lJ45RfnXNbHAQw,8923
 iplotx/layout.py,sha256=KxmRLqjo8AYCBAmXez8rIiLU2sM34qhb6ox9AHYwRyE,4839
-iplotx/network.py,sha256=5A0yvoJKAfT1xcnWYh9hHM8dkF2NkHK7RK1h9Uc35-Y,11359
-iplotx/plotting.py,sha256=yACxkD6unKc5eDsAp7ZabRCAwLEXBowSMESX2oGNBDU,7291
+iplotx/network.py,sha256=LaW9zQZ4sKiDVb25_icnquGNnN7HrKC7NO07o6PSmGI,11527
+iplotx/plotting.py,sha256=IEUxW1xzTljLjBfsVP2BNsOPCDpj5bEPZ99bzvD5-mo,10066
 iplotx/tree.py,sha256=Zzz7nCPZrSjh9_yHXFdd8hjbF-FYURTZs00rUHc4OT8,27304
 iplotx/typing.py,sha256=QLdzV358IiD1CFe88MVp0D77FSx5sSAVUmM_2WPPE8I,1463
-iplotx/version.py,sha256=4IFN3njnGdyj6gkoCknMRXJtKdrK2JFUlkOSIdsZDNM,66
-iplotx/vertex.py,sha256=AJEBtIDW0hDTij10M_hHXymVLm6iQHkQqZgVD2PllLw,14563
-iplotx/edge/__init__.py,sha256=hxRYlfWEx7DINKem9Rush9MnykRthw8jj90dsDWrK_M,27002
+iplotx/version.py,sha256=1Mi-AUAfWTkSNROfIn7bWkeZBzSl_j_A7HmbA4LSs0c,66
+iplotx/vertex.py,sha256=-JZaQPjIAWWP8Wap1HyR4g4HXLNGLwjf4v6jyo994Tk,14671
+iplotx/edge/__init__.py,sha256=HlxeIs88RbRrTetJNLcoq9gjV7cBhOdqQoiVZFFylFc,27081
 iplotx/edge/arrow.py,sha256=C4XoHGCYou1z2alz5Q2VhdaWYEzgebtEF70zVYY_frk,15533
 iplotx/edge/geometry.py,sha256=tiaF4PzvsNBoROrEgcCsw0YdxxZr3oBxF4ord_k4ThA,15069
 iplotx/edge/leaf.py,sha256=SyGMv2PIOoH0pey8-aMVaZheK3hNe1Qz_okcyWbc4E4,4268
 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=-40DsfCte65FN-FFzlvKFiLLVQGncaRNW61kitlHf9w,14086
+iplotx/ingest/typing.py,sha256=61LwNwrTHVh8eqqC778Gr81zPYcUKW61mDgGCCsuGSk,14181
 iplotx/ingest/providers/network/igraph.py,sha256=8dWeaQ_ZNdltC098V2YeLXsGdJHQnBa6shF1GAfl0Zg,2973
-iplotx/ingest/providers/network/networkx.py,sha256=FIXMI3hXU1WtAzPVlQZcz47b-4V2omeHttnNTgS2gQw,4328
+iplotx/ingest/providers/network/networkx.py,sha256=4sPFOx87ipOYlXu0hjJl25Z4So_RnhO1CYYozGp-wJg,4626
 iplotx/ingest/providers/network/simple.py,sha256=e_aHhiHhN9DrMoNrt7tEMPURXGhQ1TYRPzsxDEptUlc,3766
 iplotx/ingest/providers/tree/biopython.py,sha256=4N_54cVyHHPcASJZGr6pHKE2p5R3i8Cm307SLlSLHLA,1480
 iplotx/ingest/providers/tree/cogent3.py,sha256=JmELbDK7LyybiJzFNbmeqZ4ySJoDajvFfJebpNfFKWo,1073
@@ -33,6 +33,6 @@ iplotx/utils/geometry.py,sha256=6RrC6qaB0-1vIk1LhGA4CfsiMd-9JNniSPyL_l9mshE,9245
 iplotx/utils/internal.py,sha256=WWfcZDGK8Ut1y_tOHRGg9wSqY1bwSeLQO7dHM_8Tvwo,107
 iplotx/utils/matplotlib.py,sha256=wELE73quQv10-1w9uA5eDTgkZkylJvjg7pd3K5tZPOo,6294
 iplotx/utils/style.py,sha256=wMWxJykxBD-JmcN8-rSKlWcV6pMfwKgR4EzSpk_NX8k,547
-iplotx-0.6.5.dist-info/METADATA,sha256=0-0qPdtrERP5KY_nlerTLKWF6ykr9pQPBfIBEOo-43M,4908
-iplotx-0.6.5.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
-iplotx-0.6.5.dist-info/RECORD,,
+iplotx-0.6.7.dist-info/METADATA,sha256=O3tkLhtN4pM3FxyONC75a3CYvf1Ba6iU8bHRTgtBzgM,4908
+iplotx-0.6.7.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
+iplotx-0.6.7.dist-info/RECORD,,