removed plot_slots_graph and plot_connections_graph (now AssemblyMix …

…methods)

dnacauldron/__init__.py

@@ -34,7 +34,5 @@
 from .reports import (
     plot_cuts,
     full_assembly_report,
-    plot_slots_graph,
-    plot_connections_graph,
     full_assembly_plan_report,
 )

dnacauldron/reports/__init__.py

@@ -2,7 +2,7 @@
 
 # __all__ = []
 
-from .plots import plot_cuts, plot_slots_graph, plot_connections_graph
+from .plots import plot_cuts
 from .full_assembly_report import full_assembly_report
 from .full_assembly_plan_report import full_assembly_plan_report
 

dnacauldron/reports/full_assembly_report.py

@@ -15,9 +15,7 @@
 )
 from .plots import (
     plot_cuts,
-    plot_slots_graph,
     AssemblyTranslator,
-    plot_connections_graph,
 )
 from ..tools import write_record, record_is_linear
 

dnacauldron/reports/plots.py

@@ -9,7 +9,6 @@
     CircularGraphicRecord,
     GraphicRecord,
 )
-from matplotlib.patches import Circle
 from dnacauldron.tools import annotate_record
 
 try:
@@ -113,167 +112,4 @@ def compute_feature_color(self, feature):
     graphic_record = translator.translate_record(
         record, record_class=record_class
     )
-    return graphic_record.plot(ax=ax, figure_width=figure_width)
-
-
-def plot_slots_graph(
-    mix,
-    ax=None,
-    with_overhangs=False,
-    directed=True,
-    show_missing=True,
-    highlighted_parts=None,
-    with_arrows=True,
-):
-    """Plot a map of the different assemblies.
-
-    Parameters
-    ----------
-    mix
-      A DnaCauldron AssemblyMix object.
-
-    ax
-      A matplotlib ax on which to plot. If none is provided, one is created.
-
-    with_overhangs
-      If true, the overhangs appear in the graph
-    """
-    slots = mix.compute_slots()
-    highlighted_parts = set(
-        [] if highlighted_parts is None else highlighted_parts
-    )
-    graph = mix.slots_graph(with_overhangs=with_overhangs, directed=directed)
-
-    # Positioning - a bit complex to deal with multi-components graphs
-    pos = {}
-    undirected_graph = graph.to_undirected()
-    components = list(nx.components.connected_components(undirected_graph))
-    if components == []:
-        raise ValueError(
-            "Empty connections graph. This probably means your "
-            "parts were filtered out, possibly because they do "
-            "not contain the right enzyme sites or something "
-            "that"
-        )
-    max_len = 1.0 * max(len(c) for c in components)
-    for i, g in enumerate(components):
-        g = undirected_graph.subgraph(g)
-        pos.update(
-            nx.layout.kamada_kawai_layout(
-                g, center=(0, -i), scale=len(g) / max_len
-            )
-        )
-
-    parts = [n for n in graph.nodes() if n in slots]
-
-    fig, ax = plt.subplots(1, figsize=(13, 0.5 * len(parts)))
-    nx.draw(
-        graph,
-        pos=pos,
-        node_color="w",
-        node_size=100,
-        ax=ax,
-        edge_color="#eeeeee",
-    )
-
-    # Draw a "highlights graph" above the other graph
-    def highlight_slot(slot):
-        return any([part in highlighted_parts for part in slots.get(slot, [])])
-
-    highlighted_nodes = [n for n in graph.nodes() if highlight_slot(n)]
-    if len(highlighted_nodes):
-        highlighted_subgraph = graph.subgraph(highlighted_nodes)
-        nx.draw(
-            highlighted_subgraph,
-            pos=pos,
-            node_color="#3a3aad",
-            node_size=300,
-            ax=ax,
-            edge_color="#aaaaaa",
-        )
-    legend = []
-
-    def polar(xy):
-        x, y = xy - np.array([0.05, 0.05])
-        return (np.arctan2(x, -y), -np.sqrt(x ** 2 + y ** 2))
-
-    sorted_pos = sorted(pos.items(), key=lambda c: polar(c[1]))
-    for i, (n, (x, y)) in enumerate(sorted_pos):
-        if n in parts:
-            slot_parts = list(slots[n])
-            color = "w" if highlight_slot(n) else "#3a3aad"
-            legend.append("\n     ".join(sorted(slot_parts)))
-            fontdict = {}
-            if highlight_slot(n) or len(slot_parts) > 1:
-                fontdict = {"weight": "bold"}
-            ax.text(
-                x,
-                y,
-                len(legend),
-                ha="center",
-                va="center",
-                color=color,
-                fontdict=fontdict,
-            )
-        else:
-            ax.text(
-                x,
-                y,
-                n,
-                ha="center",
-                va="center",
-                color="#333333",
-                size=9,
-                fontdict=dict(family="Inconsolata"),
-            )
-    text = "\n".join(
-        ["Parts:"]
-        + ["%2s - %s" % (str(i + 1), name) for i, name in enumerate(legend)]
-    )
-    if show_missing:
-        all_mix_parts = set([f.id for f in mix.constructs])
-        all_slots_parts = set([p for plist in slots.values() for p in plist])
-        missing_parts = all_mix_parts.difference(all_slots_parts)
-        if len(missing_parts):
-            text += "\n!!! Missing parts: " + ", ".join(missing_parts)
-
-    ax.text(
-        1.1,
-        0.5,
-        text,
-        va="center",
-        transform=ax.transAxes,
-        fontdict=dict(size=12, family="Inconsolata"),
-    )
-    ax.set_aspect("equal")
-    return ax
-
-
-def plot_connections_graph(mix, ax=None, figsize=(20, 20)):
-
-    graph = mix.uniquified_connection_graph
-
-    def fragment_label(i):
-        fragment = mix.fragments_dict[i]
-        return "\n".join(
-            [
-                str(fragment.seq.left_end),
-                r"$\bf{%s}$" % fragment.original_construct.id,
-                str(fragment.seq.right_end),
-            ]
-        )
-
-    labels = {i: fragment_label(i) for i in graph}
-    if ax is None:
-        fig, ax = plt.subplots(1, 1, figsize=figsize)
-    nx.draw_kamada_kawai(
-        graph,
-        labels=labels,
-        font_color="k",
-        edge_color="grey",
-        font_size=12,
-        node_color="w",
-        node_size=3000,
-    )
-    return ax
-
+    return graphic_record.plot(ax=ax, figure_width=figure_width)