iplotx 0.6.6__py3-none-any.whl → 0.6.8__py3-none-any.whl

iplotx/plotting.py

@@ -29,6 +29,7 @@ def network(
     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.
@@ -55,6 +56,9 @@ def network(
             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).
@@ -71,7 +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:
@@ -135,6 +139,7 @@ def tree(
     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.
@@ -143,10 +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.
@@ -155,7 +187,7 @@ def tree(
 
     with stylecontext:
         if ax is None:
-            fig, ax = plt.subplots()
+            fig, ax = plt.subplots(figsize=figsize)
 
         artist = TreeArtist(
             tree=tree,

iplotx/tree.py

@@ -311,13 +311,21 @@ class TreeArtist(mpl.artist.Artist):
         if not leaf_style.get("deep", True):
             return
 
+        # Given the conditions above, we should have leaf labels. If not,
+        # make a None series with a valid index
+        leaf_label_series = self._get_label_series("leaf")
+        if leaf_label_series is None:
+            leaf_label_series = self._ipx_internal_data["leaf_df"].copy()
+            leaf_label_series["label"] = None
+            leaf_label_series = leaf_label_series["label"]
+
         edge_style = get_style(
             ".leafedge",
         )
         default_style = {
             "linestyle": "--",
             "linewidth": 1,
-            "edgecolor": "#111",
+            "color": "#111",
         }
         for key, value in default_style.items():
             if key not in edge_style:
@@ -335,14 +343,24 @@ class TreeArtist(mpl.artist.Artist):
         else:
             cmap_fun = None
 
-        leaf_shallow_layout = self.get_layout("leaf")
-
         if "cmap" in edge_style:
             colorarray = []
         edgepatches = []
         adjacent_vertex_ids = []
-        for i, vid in enumerate(leaf_shallow_layout.index):
-            edge_stylei = rotate_style(edge_style, index=i, key=vid)
+        for i, (vid, label) in enumerate(leaf_label_series.items()):
+            # Use leaf label to compute backup key for style rotation
+            # NOTE: This is quite a common use case. Users typically
+            # refer to leaves via their labels because that's what you see
+            # on screen. While an object exact match should take priority
+            # for power users, a backup based on label is useful. Beginners
+            # won't stumble upon this anyway since it's only used if
+            # a dict-like property for leaf edges is provided, which is a
+            # decently advanced thing to do.
+            # NOTE: Multiple leaves might have the same label, in which case
+            # all leaves will be style matched to this *unless* the dict-like
+            # style object *also* matches on leaf objects directly, which
+            # takes precedence since key2 is only a fallback.
+            edge_stylei = rotate_style(edge_style, index=i, key=vid, key2=label)
 
             if cmap_fun is not None:
                 colorarray.append(edge_stylei["color"])

iplotx/version.py

@@ -2,4 +2,4 @@
 iplotx version information module.
 """
 
-__version__ = "0.6.6"
+__version__ = "0.6.8"

{iplotx-0.6.6.dist-info → iplotx-0.6.8.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: iplotx
-Version: 0.6.6
+Version: 0.6.8
 Summary: Plot networkx from igraph and networkx.
 Project-URL: Homepage, https://github.com/fabilab/iplotx
 Project-URL: Documentation, https://readthedocs.org/iplotx

{iplotx-0.6.6.dist-info → iplotx-0.6.8.dist-info}/RECORD

@@ -5,10 +5,10 @@ iplotx/groups.py,sha256=_9KdIiTAi1kXtd2mDywgBJCbqoRq2z-5fzOPf76Wgb8,6287
 iplotx/label.py,sha256=6am3a0ejcW_bWEXSOODE1Ke3AyCU1lJ45RfnXNbHAQw,8923
 iplotx/layout.py,sha256=KxmRLqjo8AYCBAmXez8rIiLU2sM34qhb6ox9AHYwRyE,4839
 iplotx/network.py,sha256=LaW9zQZ4sKiDVb25_icnquGNnN7HrKC7NO07o6PSmGI,11527
-iplotx/plotting.py,sha256=eLsdOOZ15SQTcNeSxqpxYtzfiVPo5Npqgg5wrxyJfrs,7561
-iplotx/tree.py,sha256=Zzz7nCPZrSjh9_yHXFdd8hjbF-FYURTZs00rUHc4OT8,27304
+iplotx/plotting.py,sha256=IEUxW1xzTljLjBfsVP2BNsOPCDpj5bEPZ99bzvD5-mo,10066
+iplotx/tree.py,sha256=-69lpPjisRfigY4fDQcmVxzOAf1tGwMXviUcW6mZU6U,28508
 iplotx/typing.py,sha256=QLdzV358IiD1CFe88MVp0D77FSx5sSAVUmM_2WPPE8I,1463
-iplotx/version.py,sha256=96OI0pGtnG3BPfu9NZSoIkqwIZYegDQOF3vky5yMB_k,66
+iplotx/version.py,sha256=Ssoh-uTVPI9dHESTgtP5SAY8kO-o2pYIi_gVIxFJKiw,66
 iplotx/vertex.py,sha256=-JZaQPjIAWWP8Wap1HyR4g4HXLNGLwjf4v6jyo994Tk,14671
 iplotx/edge/__init__.py,sha256=HlxeIs88RbRrTetJNLcoq9gjV7cBhOdqQoiVZFFylFc,27081
 iplotx/edge/arrow.py,sha256=C4XoHGCYou1z2alz5Q2VhdaWYEzgebtEF70zVYY_frk,15533
@@ -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-0.6.6.dist-info/METADATA,sha256=48xdO8iccA0Y53CJLK-7xCI3rRYptFlq1MQJ_UR-cnE,4908
-iplotx-0.6.6.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
-iplotx-0.6.6.dist-info/RECORD,,
+iplotx-0.6.8.dist-info/METADATA,sha256=HorC8mcRXtF_RaDZQQbrPWtdXyBwGPTLYa5oNVViVM0,4908
+iplotx-0.6.8.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
+iplotx-0.6.8.dist-info/RECORD,,