iplotx 0.0.1__py2.py3-none-any.whl

iplotx/importing.py

@@ -0,0 +1,13 @@
+try:
+    import igraph
+except ImportError:
+    igraph = None
+
+try:
+    import networkx
+except ImportError:
+    networkx = None
+
+if igraph is None and networkx is None:
+    raise ImportError("At least one of igraph or networkx must be installed to use this module.")
+

iplotx/network.py

@@ -0,0 +1,507 @@
+from typing import Union, Sequence
+import warnings
+import numpy as np
+import pandas as pd
+import matplotlib as mpl
+from matplotlib.transforms import Affine2D
+
+from .typing import (
+    GraphType,
+    LayoutType,
+)
+from .styles import (
+    get_style,
+    rotate_style,
+)
+from .heuristics import (
+    network_library,
+    normalise_layout,
+    detect_directedness,
+)
+from .utils.matplotlib import (
+    _stale_wrapper,
+    _forwarder,
+    _get_label_width_height,
+)
+from .vertex import (
+    VertexCollection,
+    make_patch as make_vertex_patch,
+)
+from .edge.undirected import (
+    UndirectedEdgeCollection,
+    make_stub_patch as make_undirected_edge_patch,
+)
+from .edge.directed import (
+    DirectedEdgeCollection,
+    make_arrow_patch,
+)
+
+
+@_forwarder(
+    (
+        "set_clip_path",
+        "set_clip_box",
+        "set_transform",
+        "set_snap",
+        "set_sketch_params",
+        "set_figure",
+        "set_animated",
+        "set_picker",
+    )
+)
+class NetworkArtist(mpl.artist.Artist):
+    def __init__(
+        self,
+        network: GraphType,
+        layout: LayoutType = None,
+        vertex_labels: Union[None, list, dict, pd.Series] = None,
+        edge_labels: Union[None, Sequence] = None,
+    ):
+        """Network container artist that groups all plotting elements.
+
+        Parameters:
+            network (networkx.Graph or igraph.Graph): The network to plot.
+            layout (array-like): The layout of the network. If None, this function will attempt to
+                infer the layout from the network metadata, using heuristics. If that fails, an
+                exception will be raised.
+            vertex_labels (list, dict, or pandas.Series): The labels for the vertices. If None, no vertex labels
+                will be drawn. If a list, the labels are taken from the list. If a dict, the keys
+                should be the vertex IDs and the values should be the labels.
+            elge_labels (sequence): The labels for the edges. If None, no edge labels will be drawn.
+        """
+        super().__init__()
+
+        self.network = network
+        self._ipx_internal_data = _create_internal_data(
+            network,
+            layout,
+            vertex_labels=vertex_labels,
+            edge_labels=edge_labels,
+        )
+        self._clear_state()
+
+    def _clear_state(self):
+        self._vertices = None
+        self._edges = None
+        self._vertex_labels = []
+        self._edge_labels = []
+
+    def get_children(self):
+        artists = []
+        # Collect edges first. This way vertices are on top of edges,
+        # since vertices are drawn later. That is what most people expect.
+        if self._edges is not None:
+            artists.append(self._edges)
+        if self._vertices is not None:
+            artists.append(self._vertices)
+        artists.extend(self._edge_labels)
+        artists.extend(self._vertex_labels)
+        return tuple(artists)
+
+    def get_vertices(self):
+        """Get VertexCollection artist."""
+        return self._vertices
+
+    def get_edges(self):
+        """Get EdgeCollection artist."""
+        return self._edges
+
+    def get_vertex_labels(self):
+        """Get list of vertex label artists."""
+        return self._vertex_labels
+
+    def get_edge_labels(self):
+        """Get list of edge label artists."""
+        return self._edge_labels
+
+    def get_datalim(self, transData, pad=0.05):
+        """Get limits on x/y axes based on the graph layout data.
+
+        Parameters:
+            transData (Transform): The transform to use for the data.
+            pad (float): Padding to add to the limits. Default is 0.05.
+                Units are a fraction of total axis range before padding.
+        """
+        # FIXME: transData works here, but it's probably kind of broken in general
+        import numpy as np
+
+        layout_columns = [
+            f"_ipx_layout_{i}" for i in range(self._ipx_internal_data["ndim"])
+        ]
+        layout = self._ipx_internal_data["vertex_df"][layout_columns].values
+
+        if len(layout) == 0:
+            mins = np.array([0, 0])
+            maxs = np.array([1, 1])
+            return (mins, maxs)
+
+        # Use the layout as a base, and expand using bboxes from other artists
+        mins = np.min(layout, axis=0).astype(float)
+        maxs = np.max(layout, axis=0).astype(float)
+
+        # NOTE: unlike other Collections, the vertices are basically a
+        # PatchCollection with an offset transform using transData. Therefore,
+        # care should be taken if one wants to include it here
+        if self._vertices is not None:
+            trans = transData.transform
+            trans_inv = transData.inverted().transform
+            verts = self._vertices
+            for path, offset in zip(verts.get_paths(), verts._offsets):
+                bbox = path.get_extents()
+                mins = np.minimum(mins, trans_inv(bbox.min + trans(offset)))
+                maxs = np.maximum(maxs, trans_inv(bbox.max + trans(offset)))
+
+        if self._edges is not None:
+            for path in self._edges.get_paths():
+                bbox = path.get_extents()
+                mins = np.minimum(mins, bbox.min)
+                maxs = np.maximum(maxs, bbox.max)
+
+        if hasattr(self, "_groups") and self._groups is not None:
+            for path in self._groups.get_paths():
+                bbox = path.get_extents()
+                mins = np.minimum(mins, bbox.min)
+                maxs = np.maximum(maxs, bbox.max)
+
+        # 5% padding, on each side
+        pad = (maxs - mins) * pad
+        mins -= pad
+        maxs += pad
+
+        return mpl.transforms.Bbox([mins, maxs])
+
+    def _add_vertices(self):
+        """Draw the vertices"""
+        vertex_style = get_style(".vertex")
+
+        layout_columns = [
+            f"_ipx_layout_{i}" for i in range(self._ipx_internal_data["ndim"])
+        ]
+        vertex_layout_df = self._ipx_internal_data["vertex_df"][layout_columns]
+        if vertex_style.get("size") == "label":
+            if "label" not in self._ipx_internal_data["vertex_df"].columns:
+                warnings.warn(
+                    "No labels found, cannot resize vertices based on labels."
+                )
+                vertex_style["size"] = get_style("default.vertex")["size"]
+            else:
+                vertex_labels = self._ipx_internal_data["vertex_df"]["label"]
+
+        # FIXME:: this would be better off in the VertexCollection itself, like we do for groups
+        offsets = []
+        patches = []
+        for i, (vid, row) in enumerate(vertex_layout_df.iterrows()):
+            # Centre of the vertex
+            offsets.append(list(row[layout_columns].values))
+
+            if vertex_style.get("size") == "label":
+                # NOTE: it's ok to overwrite the dict here
+                vertex_style["size"] = _get_label_width_height(
+                    vertex_labels[vid], **vertex_style.get("label", {})
+                )
+
+            vertex_stylei = rotate_style(vertex_style, index=i, id=vid)
+
+            # Shape of the vertex (Patch)
+            art = make_vertex_patch(**vertex_stylei)
+            patches.append(art)
+
+        art = VertexCollection(
+            patches,
+            offsets=offsets if offsets else None,
+            offset_transform=self.axes.transData,
+            transform=Affine2D(),
+            match_original=True,
+        )
+        self._vertices = art
+
+    def _add_vertex_labels(self):
+        """Draw vertex labels."""
+        label_style = get_style(".vertex.label")
+        forbidden_props = ["hpadding", "vpadding"]
+        for prop in forbidden_props:
+            if prop in label_style:
+                del label_style[prop]
+
+        texts = []
+        vertex_labels = self._ipx_internal_data["vertex_df"]["label"]
+        for offset, label in zip(self._vertices._offsets, vertex_labels):
+            text = mpl.text.Text(
+                offset[0],
+                offset[1],
+                label,
+                transform=self.axes.transData,
+                **label_style,
+            )
+            texts.append(text)
+        self._vertex_labels = texts
+
+    def _add_edges(self):
+        """Draw the edges."""
+        if "labels" in self._ipx_internal_data["edge_df"].columns:
+            labels = self._ipx_internal_data["edge_df"]["labels"]
+        else:
+            labels = None
+
+        if self._ipx_internal_data["directed"]:
+            return self._add_directed_edges(labels=labels)
+        return self._add_undirected_edges(labels=labels)
+
+    def _add_directed_edges(self, labels=None):
+        """Draw directed edges."""
+        edge_style = get_style(".edge")
+        arrow_style = get_style(".arrow")
+
+        layout_columns = [
+            f"_ipx_layout_{i}" for i in range(self._ipx_internal_data["ndim"])
+        ]
+        vertex_layout_df = self._ipx_internal_data["vertex_df"][layout_columns]
+        edge_df = self._ipx_internal_data["edge_df"].set_index(
+            ["_ipx_source", "_ipx_target"]
+        )
+
+        # This contains the patches for vertices, for edge shortening and such
+        vertex_paths = self._vertices._paths
+        vertex_indices = pd.Series(
+            np.arange(len(vertex_layout_df)), index=vertex_layout_df.index
+        )
+
+        edgepatches = []
+        arrowpatches = []
+        adjacent_vertex_ids = []
+        adjecent_vertex_centers = []
+        adjecent_vertex_paths = []
+        for i, (vid1, vid2) in enumerate(edge_df.index):
+            # Get the vertices for this edge
+            vcenter1 = vertex_layout_df.loc[vid1, layout_columns].values
+            vcenter2 = vertex_layout_df.loc[vid2, layout_columns].values
+            vpath1 = vertex_paths[vertex_indices[vid1]]
+            vpath2 = vertex_paths[vertex_indices[vid2]]
+
+            edge_stylei = rotate_style(edge_style, index=i, id=(vid1, vid2))
+
+            # These are not the actual edges drawn, only stubs to establish
+            # the styles which are then fed into the dynamic, optimised
+            # factory (the collection) below
+            patch = make_undirected_edge_patch(
+                **edge_stylei,
+            )
+            edgepatches.append(patch)
+            adjacent_vertex_ids.append((vid1, vid2))
+            adjecent_vertex_centers.append((vcenter1, vcenter2))
+            adjecent_vertex_paths.append((vpath1, vpath2))
+
+            arrow_patch = make_arrow_patch(
+                **arrow_style,
+            )
+            arrowpatches.append(arrow_patch)
+
+        adjacent_vertex_ids = np.array(adjacent_vertex_ids)
+        adjecent_vertex_centers = np.array(adjecent_vertex_centers)
+        # NOTE: the paths might have different number of sides, so it cannot be recast
+
+        # TODO:: deal with "ports" a la graphviz
+
+        art = DirectedEdgeCollection(
+            edges=edgepatches,
+            arrows=arrowpatches,
+            labels=labels,
+            vertex_ids=adjacent_vertex_ids,
+            vertex_paths=adjecent_vertex_paths,
+            vertex_centers=adjecent_vertex_centers,
+            transform=self.axes.transData,
+            style=edge_style,
+        )
+        self._edges = art
+
+    def _add_undirected_edges(self, labels=None):
+        """Draw undirected edges."""
+        edge_style = get_style(".edge")
+
+        layout_columns = [
+            f"_ipx_layout_{i}" for i in range(self._ipx_internal_data["ndim"])
+        ]
+        vertex_layout_df = self._ipx_internal_data["vertex_df"][layout_columns]
+        edge_df = self._ipx_internal_data["edge_df"].set_index(
+            ["_ipx_source", "_ipx_target"]
+        )
+
+        # This contains the patches for vertices, for edge shortening and such
+        vertex_paths = self._vertices._paths
+        vertex_indices = pd.Series(
+            np.arange(len(vertex_layout_df)), index=vertex_layout_df.index
+        )
+
+        edgepatches = []
+        adjacent_vertex_ids = []
+        adjecent_vertex_centers = []
+        adjecent_vertex_paths = []
+        for i, (vid1, vid2) in enumerate(edge_df.index):
+            # Get the vertices for this edge
+            vcenter1 = vertex_layout_df.loc[vid1, layout_columns].values
+            vcenter2 = vertex_layout_df.loc[vid2, layout_columns].values
+            vpath1 = vertex_paths[vertex_indices[vid1]]
+            vpath2 = vertex_paths[vertex_indices[vid2]]
+
+            edge_stylei = rotate_style(edge_style, index=i, id=(vid1, vid2))
+
+            # These are not the actual edges drawn, only stubs to establish
+            # the styles which are then fed into the dynamic, optimised
+            # factory (the collection) below
+            patch = make_undirected_edge_patch(
+                **edge_stylei,
+            )
+            edgepatches.append(patch)
+            adjacent_vertex_ids.append((vid1, vid2))
+            adjecent_vertex_centers.append((vcenter1, vcenter2))
+            adjecent_vertex_paths.append((vpath1, vpath2))
+
+        adjacent_vertex_ids = np.array(adjacent_vertex_ids)
+        adjecent_vertex_centers = np.array(adjecent_vertex_centers)
+        # NOTE: the paths might have different number of sides, so it cannot be recast
+
+        # TODO:: deal with "ports" a la graphviz
+
+        art = UndirectedEdgeCollection(
+            edgepatches,
+            labels=labels,
+            vertex_ids=adjacent_vertex_ids,
+            vertex_paths=adjecent_vertex_paths,
+            vertex_centers=adjecent_vertex_centers,
+            transform=self.axes.transData,
+            style=edge_style,
+        )
+        self._edges = art
+
+    def _process(self):
+        self._clear_state()
+
+        # TODO: some more things might be plotted before this
+
+        # NOTE: we plot vertices first to get size etc. for edge shortening
+        # but when the mpl engine runs down all children artists for actual
+        # drawing it uses get_children() to get the order. Whatever is last
+        # in that order will get drawn on top (vis-a-vis zorder).
+        self._add_vertices()
+        self._add_edges()
+        if "label" in self._ipx_internal_data["vertex_df"].columns:
+            self._add_vertex_labels()
+
+        # TODO: callbacks for stale vertices/edges
+
+        # Forward mpl properties to children
+        # TODO sort out all of the things that need to be forwarded
+        for child in self.get_children():
+            # set the figure & axes on child, this ensures each artist
+            # down the hierarchy knows where to draw
+            if hasattr(child, "set_figure"):
+                child.set_figure(self.figure)
+            child.axes = self.axes
+
+            # forward the clippath/box to the children need this logic
+            # because mpl exposes some fast-path logic
+            clip_path = self.get_clip_path()
+            if clip_path is None:
+                clip_box = self.get_clip_box()
+                child.set_clip_box(clip_box)
+            else:
+                child.set_clip_path(clip_path)
+
+    @_stale_wrapper
+    def draw(self, renderer, *args, **kwds):
+        """Draw each of the children, with some buffering mechanism."""
+        if not self.get_visible():
+            return
+
+        if not self.get_children():
+            self._process()
+
+        # NOTE: looks like we have to manage the zorder ourselves
+        # this is kind of funny actually
+        children = list(self.get_children())
+        children.sort(key=lambda x: x.zorder)
+        for art in children:
+            art.draw(renderer, *args, **kwds)
+
+
+# INTERNAL ROUTINES
+def _create_internal_data(
+    network,
+    layout=None,
+    vertex_labels=None,
+    edge_labels=None,
+):
+    """Create internal data for the network."""
+    nl = network_library(network)
+    directed = detect_directedness(network)
+
+    if nl == "networkx":
+        # Vertices are indexed by node ID
+        vertex_df = normalise_layout(layout).loc[pd.Index(network.nodes)]
+        ndim = vertex_df.shape[1]
+        vertex_df.columns = [f"_ipx_layout_{i}" for i in range(ndim)]
+
+        # Vertex labels
+        if vertex_labels is not None:
+            if len(vertex_labels) != len(vertex_df):
+                raise ValueError(
+                    "Vertex labels must be the same length as the number of vertices."
+                )
+            vertex_df["label"] = vertex_labels
+
+        # Edges are a list of tuples, because of multiedges
+        tmp = []
+        for u, v, d in network.edges.data():
+            row = {"_ipx_source": u, "_ipx_target": v}
+            row.update(d)
+            tmp.append(row)
+        edge_df = pd.DataFrame(tmp)
+        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["labels"] = edge_labels
+
+    else:
+        # Vertices are ordered integers, no gaps
+        vertex_df = normalise_layout(layout)
+        ndim = vertex_df.shape[1]
+        vertex_df.columns = [f"_ipx_layout_{i}" for i in range(ndim)]
+
+        # Vertex labels
+        if vertex_labels is not None:
+            if len(vertex_labels) != len(vertex_df):
+                raise ValueError(
+                    "Vertex labels must be the same length as the number of vertices."
+                )
+            vertex_df["label"] = vertex_labels
+
+        # Edges are a list of tuples, because of multiedges
+        tmp = []
+        for edge in network.es:
+            row = {"_ipx_source": edge.source, "_ipx_target": edge.target}
+            row.update(edge.attributes())
+            tmp.append(row)
+        edge_df = pd.DataFrame(tmp)
+        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["labels"] = edge_labels
+
+    internal_data = {
+        "vertex_df": vertex_df,
+        "edge_df": edge_df,
+        "directed": directed,
+        "network_library": nl,
+        "ndim": ndim,
+    }
+    return internal_data

iplotx/plotting.py

@@ -0,0 +1,104 @@
+from typing import Union, Sequence
+import pandas as pd
+import matplotlib as mpl
+import matplotlib.pyplot as plt
+
+from .typing import (
+    GraphType,
+    LayoutType,
+    GroupingType,
+)
+from .network import NetworkArtist
+from .groups import GroupingArtist
+from .styles import stylecontext
+
+
+def plot(
+    network: Union[GraphType, None] = None,
+    layout: Union[LayoutType, None] = None,
+    grouping: Union[None, GroupingType] = None,
+    vertex_labels: Union[None, list, dict, pd.Series] = None,
+    edge_labels: Union[None, Sequence] = None,
+    ax: Union[None, object] = None,
+    styles: Sequence[Union[str, dict]] = (),
+):
+    """Plot this network using the specified layout.
+
+    Parameters:
+        network (GraphType): The network to plot. Can be a networkx or igraph graph.
+        layout (Union[LayoutType, None], optional): The layout to use for plotting. If None, a layout will be looked for in the network object and, if none is found, an exception is raised. Defaults to None.
+        vertex_labels (list, dict, or pandas.Series): The labels for the vertices. If None, no vertex labels
+            will be drawn. If a list, the labels are taken from the list. If a dict, the keys
+            should be the vertex IDs and the values should be the labels.
+        edge_labels (Union[None, Sequence], optional): The labels for the edges. If None, no edge labels will be drawn. Defaults to None.
+        ax (Union[None, object], optional): The axis to plot on. If None, a new figure and axis will be created. Defaults to None.
+        **style: Additional keyword arguments are treated as style for the objects to plot.
+
+    Returns:
+        A NetworkArtist object.
+    """
+    if len(styles):
+        with stylecontext(styles):
+            return plot(
+                network=network,
+                layout=layout,
+                grouping=grouping,
+                edge_labels=edge_labels,
+            )
+
+    if (network is None) and (grouping is None):
+        raise ValueError("At least one of network or grouping must be provided.")
+
+    if ax is None:
+        fig, ax = plt.subplots()
+
+    artists = []
+    if network is not None:
+        nwkart = NetworkArtist(
+            network,
+            layout,
+            vertex_labels=vertex_labels,
+            edge_labels=edge_labels,
+        )
+        ax.add_artist(nwkart)
+        # Postprocess for things that require an axis (transform, etc.)
+        nwkart._process()
+        artists.append(nwkart)
+
+    if grouping is not None:
+        grpart = GroupingArtist(
+            grouping,
+            layout,
+        )
+        ax.add_artist(grpart)
+        # Postprocess for things that require an axis (transform, etc.)
+        grpart._process()
+        artists.append(grpart)
+
+    _postprocess_axis(ax, artists)
+
+    return artists
+
+
+# INTERNAL ROUTINES
+def _postprocess_axis(ax, artists):
+    """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)
+
+    # Remove axis ticks
+    ax.set_xticks([])
+    ax.set_yticks([])
+
+    # Set new data limits
+    bboxes = []
+    for art in artists:
+        bboxes.append(art.get_datalim(ax.transData))
+    ax.update_datalim(mpl.transforms.Bbox.union(bboxes))
+
+    # Autoscale for x/y axis limits
+    ax.autoscale_view()