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Deltares-research · Apr 12, 2024 · cdbcf64 · cdbcf64
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diff --git a/documentation/develop/example/ex_05_sequence_graph/05_plot_serial_sequence_graph.py b/documentation/develop/example/ex_05_sequence_graph/05_plot_serial_sequence_graph.py
@@ -9,8 +9,7 @@
 
 from adaptation_pathways.graph import SequenceGraph
 from adaptation_pathways.io import text
-from adaptation_pathways.plot import init_axes
-from adaptation_pathways.plot import plot_default_sequence_graph as plot
+from adaptation_pathways.plot import init_axes, plot_default_sequence_graph
 
 
 actions, colour_by_action = text.read_actions(
@@ -44,5 +43,5 @@
 
 _, axes = plt.subplots(layout="constrained")
 init_axes(axes)
-plot(axes, sequence_graph)
+plot_default_sequence_graph(axes, sequence_graph)
 plt.show()
diff --git a/documentation/develop/example/ex_05_sequence_graph/10_plot_diverging_sequence_graph.py b/documentation/develop/example/ex_05_sequence_graph/10_plot_diverging_sequence_graph.py
@@ -9,8 +9,7 @@
 
 from adaptation_pathways.graph import SequenceGraph
 from adaptation_pathways.io import text
-from adaptation_pathways.plot import init_axes
-from adaptation_pathways.plot import plot_default_sequence_graph as plot
+from adaptation_pathways.plot import init_axes, plot_default_sequence_graph
 
 
 actions, colour_by_action = text.read_actions(
@@ -44,5 +43,5 @@
 
 _, axes = plt.subplots(layout="constrained")
 init_axes(axes)
-plot(axes, sequence_graph)
+plot_default_sequence_graph(axes, sequence_graph)
 plt.show()
diff --git a/documentation/develop/example/ex_05_sequence_graph/15_plot_converging_sequence_graph.py b/documentation/develop/example/ex_05_sequence_graph/15_plot_converging_sequence_graph.py
@@ -9,8 +9,7 @@
 
 from adaptation_pathways.graph import SequenceGraph
 from adaptation_pathways.io import text
-from adaptation_pathways.plot import init_axes
-from adaptation_pathways.plot import plot_default_sequence_graph as plot
+from adaptation_pathways.plot import init_axes, plot_default_sequence_graph
 
 
 actions, colour_by_action = text.read_actions(
@@ -48,5 +47,5 @@
 
 _, axes = plt.subplots(layout="constrained")
 init_axes(axes)
-plot(axes, sequence_graph)
+plot_default_sequence_graph(axes, sequence_graph)
 plt.show()
diff --git a/documentation/develop/example/ex_05_sequence_graph/20_plot_example_sequence_graph.py b/documentation/develop/example/ex_05_sequence_graph/20_plot_example_sequence_graph.py
@@ -9,8 +9,7 @@
 
 from adaptation_pathways.graph import SequenceGraph
 from adaptation_pathways.io import text
-from adaptation_pathways.plot import init_axes
-from adaptation_pathways.plot import plot_default_sequence_graph as plot
+from adaptation_pathways.plot import init_axes, plot_default_sequence_graph
 
 
 actions, colour_by_action = text.read_actions(
@@ -55,5 +54,5 @@
 
 _, axes = plt.subplots(layout="constrained")
 init_axes(axes)
-plot(axes, sequence_graph)
+plot_default_sequence_graph(axes, sequence_graph)
 plt.show()
diff --git a/documentation/develop/example/ex_05_sequence_graph/25_plot_example_sequence_graph.py b/documentation/develop/example/ex_05_sequence_graph/25_plot_example_sequence_graph.py
@@ -9,8 +9,7 @@
 
 from adaptation_pathways.graph import SequenceGraph
 from adaptation_pathways.io import text
-from adaptation_pathways.plot import init_axes
-from adaptation_pathways.plot import plot_default_sequence_graph as plot
+from adaptation_pathways.plot import init_axes, plot_default_sequence_graph
 
 
 actions, colour_by_action = text.read_actions(
@@ -61,5 +60,5 @@
 
 _, axes = plt.subplots(layout="constrained")
 init_axes(axes)
-plot(axes, sequence_graph)
+plot_default_sequence_graph(axes, sequence_graph)
 plt.show()
diff --git a/documentation/develop/example/ex_10_pathway_graph/05_plot_serial_pathway_graph.py b/documentation/develop/example/ex_10_pathway_graph/05_plot_serial_pathway_graph.py
@@ -9,8 +9,7 @@
 
 from adaptation_pathways.graph import SequenceGraph, sequence_graph_to_pathway_graph
 from adaptation_pathways.io import text
-from adaptation_pathways.plot import init_axes
-from adaptation_pathways.plot import plot_default_pathway_graph as plot
+from adaptation_pathways.plot import init_axes, plot_default_pathway_graph
 
 
 actions, colour_by_action = text.read_actions(
@@ -45,5 +44,5 @@
 
 _, axes = plt.subplots(layout="constrained")
 init_axes(axes)
-plot(axes, pathway_graph)
+plot_default_pathway_graph(axes, pathway_graph)
 plt.show()
diff --git a/documentation/develop/example/ex_10_pathway_graph/10_plot_diverging_pathway_graph.py b/documentation/develop/example/ex_10_pathway_graph/10_plot_diverging_pathway_graph.py
@@ -9,8 +9,7 @@
 
 from adaptation_pathways.graph import SequenceGraph, sequence_graph_to_pathway_graph
 from adaptation_pathways.io import text
-from adaptation_pathways.plot import init_axes
-from adaptation_pathways.plot import plot_default_pathway_graph as plot
+from adaptation_pathways.plot import init_axes, plot_default_pathway_graph
 
 
 actions, colour_by_action = text.read_actions(
@@ -45,5 +44,5 @@
 
 _, axes = plt.subplots(layout="constrained")
 init_axes(axes)
-plot(axes, pathway_graph)
+plot_default_pathway_graph(axes, pathway_graph)
 plt.show()
diff --git a/documentation/develop/example/ex_10_pathway_graph/15_plot_converging_pathway_graph.py b/documentation/develop/example/ex_10_pathway_graph/15_plot_converging_pathway_graph.py
@@ -9,8 +9,7 @@
 
 from adaptation_pathways.graph import SequenceGraph, sequence_graph_to_pathway_graph
 from adaptation_pathways.io import text
-from adaptation_pathways.plot import init_axes
-from adaptation_pathways.plot import plot_default_pathway_graph as plot
+from adaptation_pathways.plot import init_axes, plot_default_pathway_graph
 
 
 actions, colour_by_action = text.read_actions(
@@ -49,5 +48,5 @@
 
 _, axes = plt.subplots(layout="constrained")
 init_axes(axes)
-plot(axes, pathway_graph)
+plot_default_pathway_graph(axes, pathway_graph)
 plt.show()
diff --git a/documentation/develop/example/ex_10_pathway_graph/20_plot_example_pathway_graph.py b/documentation/develop/example/ex_10_pathway_graph/20_plot_example_pathway_graph.py
@@ -9,8 +9,7 @@
 
 from adaptation_pathways.graph import SequenceGraph, sequence_graph_to_pathway_graph
 from adaptation_pathways.io import text
-from adaptation_pathways.plot import init_axes
-from adaptation_pathways.plot import plot_default_pathway_graph as plot
+from adaptation_pathways.plot import init_axes, plot_default_pathway_graph
 
 
 actions, colour_by_action = text.read_actions(
@@ -56,5 +55,5 @@
 
 _, axes = plt.subplots(layout="constrained")
 init_axes(axes)
-plot(axes, pathway_graph)
+plot_default_pathway_graph(axes, pathway_graph)
 plt.show()
diff --git a/documentation/develop/example/ex_10_pathway_graph/25_plot_example_pathway_graph.py b/documentation/develop/example/ex_10_pathway_graph/25_plot_example_pathway_graph.py
@@ -9,8 +9,7 @@
 
 from adaptation_pathways.graph import SequenceGraph, sequence_graph_to_pathway_graph
 from adaptation_pathways.io import text
-from adaptation_pathways.plot import init_axes
-from adaptation_pathways.plot import plot_default_pathway_graph as plot
+from adaptation_pathways.plot import init_axes, plot_default_pathway_graph
 
 
 actions, colour_by_action = text.read_actions(
@@ -62,5 +61,5 @@
 
 _, axes = plt.subplots(layout="constrained")
 init_axes(axes)
-plot(axes, pathway_graph)
+plot_default_pathway_graph(axes, pathway_graph)
 plt.show()
diff --git a/documentation/develop/example/ex_15_pathway_map/05_plot_serial_pathway_map.py b/documentation/develop/example/ex_15_pathway_map/05_plot_serial_pathway_map.py
@@ -9,8 +9,7 @@
 
 from adaptation_pathways.graph import SequenceGraph, sequence_graph_to_pathway_map
 from adaptation_pathways.io import text
-from adaptation_pathways.plot import init_axes
-from adaptation_pathways.plot import plot_default_pathway_map as plot
+from adaptation_pathways.plot import init_axes, plot_default_pathway_map
 
 
 actions, colour_by_action = text.read_actions(
@@ -45,5 +44,5 @@
 
 _, axes = plt.subplots(layout="constrained")
 init_axes(axes)
-plot(axes, pathway_map)
+plot_default_pathway_map(axes, pathway_map)
 plt.show()
diff --git a/documentation/develop/example/ex_15_pathway_map/10_plot_diverging_pathway_map.py b/documentation/develop/example/ex_15_pathway_map/10_plot_diverging_pathway_map.py
@@ -9,8 +9,7 @@
 
 from adaptation_pathways.graph import SequenceGraph, sequence_graph_to_pathway_map
 from adaptation_pathways.io import text
-from adaptation_pathways.plot import init_axes
-from adaptation_pathways.plot import plot_default_pathway_map as plot
+from adaptation_pathways.plot import init_axes, plot_default_pathway_map
 
 
 actions, colour_by_action = text.read_actions(
@@ -45,5 +44,5 @@
 
 _, axes = plt.subplots(layout="constrained")
 init_axes(axes)
-plot(axes, pathway_map)
+plot_default_pathway_map(axes, pathway_map)
 plt.show()
diff --git a/documentation/develop/example/ex_15_pathway_map/15_plot_converging_pathway_map.py b/documentation/develop/example/ex_15_pathway_map/15_plot_converging_pathway_map.py
@@ -9,8 +9,7 @@
 
 from adaptation_pathways.graph import SequenceGraph, sequence_graph_to_pathway_map
 from adaptation_pathways.io import text
-from adaptation_pathways.plot import init_axes
-from adaptation_pathways.plot import plot_default_pathway_map as plot
+from adaptation_pathways.plot import init_axes, plot_default_pathway_map
 
 
 actions, colour_by_action = text.read_actions(
@@ -49,5 +48,5 @@
 
 _, axes = plt.subplots(layout="constrained")
 init_axes(axes)
-plot(axes, pathway_map)
+plot_default_pathway_map(axes, pathway_map)
 plt.show()
diff --git a/documentation/develop/example/ex_15_pathway_map/20_plot_example_pathway_map.py b/documentation/develop/example/ex_15_pathway_map/20_plot_example_pathway_map.py
@@ -9,8 +9,7 @@
 
 from adaptation_pathways.graph import SequenceGraph, sequence_graph_to_pathway_map
 from adaptation_pathways.io import text
-from adaptation_pathways.plot import init_axes
-from adaptation_pathways.plot import plot_default_pathway_map as plot
+from adaptation_pathways.plot import init_axes, plot_default_pathway_map
 
 
 actions, colour_by_action = text.read_actions(
@@ -56,5 +55,5 @@
 
 _, axes = plt.subplots(layout="constrained")
 init_axes(axes)
-plot(axes, pathway_map)
+plot_default_pathway_map(axes, pathway_map)
 plt.show()
diff --git a/documentation/develop/example/ex_15_pathway_map/25_plot_example_pathway_map.py b/documentation/develop/example/ex_15_pathway_map/25_plot_example_pathway_map.py
@@ -9,8 +9,7 @@
 
 from adaptation_pathways.graph import SequenceGraph, sequence_graph_to_pathway_map
 from adaptation_pathways.io import text
-from adaptation_pathways.plot import init_axes
-from adaptation_pathways.plot import plot_default_pathway_map as plot
+from adaptation_pathways.plot import init_axes, plot_default_pathway_map
 
 
 actions, colour_by_action = text.read_actions(
@@ -62,5 +61,5 @@
 
 _, axes = plt.subplots(layout="constrained")
 init_axes(axes)
-plot(axes, pathway_map)
+plot_default_pathway_map(axes, pathway_map)
 plt.show()
diff --git a/documentation/use/example/ex_10_pathway_map/05_plot_serial_pathway_map_classic.py b/documentation/use/example/ex_10_pathway_map/05_plot_serial_pathway_map_classic.py
@@ -9,8 +9,11 @@
 
 from adaptation_pathways.graph import SequenceGraph, sequence_graph_to_pathway_map
 from adaptation_pathways.io import text
-from adaptation_pathways.plot import action_level_by_first_occurrence, init_axes
-from adaptation_pathways.plot import plot_classic_pathway_map as plot
+from adaptation_pathways.plot import (
+    action_level_by_first_occurrence,
+    init_axes,
+    plot_classic_pathway_map,
+)
 
 
 actions, colour_by_action = text.read_actions(
@@ -48,5 +51,5 @@
 
 _, axes = plt.subplots(layout="constrained")
 init_axes(axes)
-plot(axes, pathway_map)
+plot_classic_pathway_map(axes, pathway_map)
 plt.show()
diff --git a/documentation/use/example/ex_10_pathway_map/10_plot_diverging_pathway_map_classic.py b/documentation/use/example/ex_10_pathway_map/10_plot_diverging_pathway_map_classic.py
@@ -9,8 +9,11 @@
 
 from adaptation_pathways.graph import SequenceGraph, sequence_graph_to_pathway_map
 from adaptation_pathways.io import text
-from adaptation_pathways.plot import action_level_by_first_occurrence, init_axes
-from adaptation_pathways.plot import plot_classic_pathway_map as plot
+from adaptation_pathways.plot import (
+    action_level_by_first_occurrence,
+    init_axes,
+    plot_classic_pathway_map,
+)
 
 
 actions, colour_by_action = text.read_actions(
@@ -48,5 +51,5 @@
 
 _, axes = plt.subplots(layout="constrained")
 init_axes(axes)
-plot(axes, pathway_map)
+plot_classic_pathway_map(axes, pathway_map)
 plt.show()
diff --git a/documentation/use/example/ex_10_pathway_map/15_plot_converging_pathway_map_classic.py b/documentation/use/example/ex_10_pathway_map/15_plot_converging_pathway_map_classic.py
@@ -9,8 +9,11 @@
 
 from adaptation_pathways.graph import SequenceGraph, sequence_graph_to_pathway_map
 from adaptation_pathways.io import text
-from adaptation_pathways.plot import action_level_by_first_occurrence, init_axes
-from adaptation_pathways.plot import plot_classic_pathway_map as plot
+from adaptation_pathways.plot import (
+    action_level_by_first_occurrence,
+    init_axes,
+    plot_classic_pathway_map,
+)
 
 
 actions, colour_by_action = text.read_actions(
@@ -52,5 +55,5 @@
 
 _, axes = plt.subplots(layout="constrained")
 init_axes(axes)
-plot(axes, pathway_map)
+plot_classic_pathway_map(axes, pathway_map)
 plt.show()
diff --git a/documentation/use/example/ex_10_pathway_map/20_plot_example_pathway_map_classic.py b/documentation/use/example/ex_10_pathway_map/20_plot_example_pathway_map_classic.py
@@ -9,8 +9,11 @@
 
 from adaptation_pathways.graph import SequenceGraph, sequence_graph_to_pathway_map
 from adaptation_pathways.io import text
-from adaptation_pathways.plot import action_level_by_first_occurrence, init_axes
-from adaptation_pathways.plot import plot_classic_pathway_map as plot
+from adaptation_pathways.plot import (
+    action_level_by_first_occurrence,
+    init_axes,
+    plot_classic_pathway_map,
+)
 
 
 actions, colour_by_action = text.read_actions(
@@ -59,5 +62,5 @@
 
 _, axes = plt.subplots(layout="constrained")
 init_axes(axes)
-plot(axes, pathway_map)
+plot_classic_pathway_map(axes, pathway_map)
 plt.show()
diff --git a/documentation/use/example/ex_10_pathway_map/25_plot_example_pathway_map_classic.py b/documentation/use/example/ex_10_pathway_map/25_plot_example_pathway_map_classic.py
@@ -9,8 +9,11 @@
 
 from adaptation_pathways.graph import SequenceGraph, sequence_graph_to_pathway_map
 from adaptation_pathways.io import text
-from adaptation_pathways.plot import action_level_by_first_occurrence, init_axes
-from adaptation_pathways.plot import plot_classic_pathway_map as plot
+from adaptation_pathways.plot import (
+    action_level_by_first_occurrence,
+    init_axes,
+    plot_classic_pathway_map,
+)
 
 
 actions, colour_by_action = text.read_actions(
@@ -65,5 +68,5 @@
 
 _, axes = plt.subplots(layout="constrained")
 init_axes(axes)
-plot(axes, pathway_map)
+plot_classic_pathway_map(axes, pathway_map)
 plt.show()
diff --git a/documentation/use/plot.rst b/documentation/use/plot.rst
@@ -10,7 +10,7 @@ Plotting pathways
 The package contains two command-line applications. One is called ``ap_plot_graphs`` and can
 be used to gain insight into various kinds of graphs used to store information about pathways,
 and one is called ``ap_plot_pathway_map`` and can be used to visualize pathway maps in the
-so-called :const:`CLASSIC <adaptation_pathways.plot.util.PathwayMapLayout.CLASSIC>` layout.
+so-called :const:`CLASSIC <adaptation_pathways.plot.pathway_map.plot.PathwayMapLayout.CLASSIC>` layout.
 
 
 ``ap_plot_graphs``
@@ -23,7 +23,7 @@ See also:
 
 This command takes information about pathways as input, and outputs a plot of the sequence
 graph, a plot of the pathway graph and a plot of the pathway map in :const:`DEFAULT
-<adaptation_pathways.plot.util.PathwayMapLayout.DEFAULT>` layout.
+<adaptation_pathways.plot.pathway_map.plot.PathwayMapLayout.DEFAULT>` layout.
 
 Example for creating plots from ``my_pathways-action.txt`` and ``my_pathways-sequence.txt``
 (or ``my_pathways.apw``) to ``./my_pathways-sequence_graph.pdf``,
@@ -43,7 +43,7 @@ See also:
 :class:`PathwayMap <adaptation_pathways.graph.pathway_map.PathwayMap>`
 
 This command takes information about pathways as input, and outputs a single plot containing
-the pathway map in :const:`CLASSIC <adaptation_pathways.plot.util.PathwayMapLayout.CLASSIC>`
+the pathway map in :const:`CLASSIC <adaptation_pathways.plot.pathway_map.plot.PathwayMapLayout.CLASSIC>`
 layout.
 
 Example for creating a plot from ``my_pathways-action.txt`` and ``my_pathways-sequence.txt``