Merge pull request #70 from geoneric/gh67

Add plot to visualize pathways using horizontal bars

documentation/use/example/README.rst

@@ -3,4 +3,4 @@ Examples
 
 This section contains examples for plotting pathway maps using the ``adaptation_pathways``
 package. The same plots can be created by storing the information about the actions and sequences
-in a text- or binary-formatted dataset and using the ``ap_plot_pathway_map`` command.
+in a text- or binary-formatted dataset and using the ``ap_plot_pathway_map`` and ``ap_plot_bars`` commands.

documentation/use/example/ex_15_bar_plot/05_plot_serial_bar_plot.py

@@ -0,0 +1,58 @@
+"""
+Bar plot for serial sequence
+============================
+"""
+
+from io import StringIO
+
+import matplotlib.pyplot as plt
+
+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,
+    plot_bars,
+)
+
+
+actions, colour_by_action = text.read_actions(
+    StringIO(
+        """
+current #ff4c566a
+a #ffbf616a
+b #ffd08770
+c #ffebcb8b
+"""
+    )
+)
+sequences, tipping_point_by_action = text.read_sequences(
+    StringIO(
+        """
+current current 2030
+current a 2040
+a b 2050
+b c 2060
+"""
+    ),
+    actions,
+)
+sequence_graph = SequenceGraph(sequences)
+pathway_map = sequence_graph_to_pathway_map(sequence_graph)
+
+level_by_action = action_level_by_first_occurrence(sequences)
+colour_by_action_name = {
+    action.name: colour for action, colour in colour_by_action.items()
+}
+
+pathway_map.assign_tipping_points(tipping_point_by_action)
+pathway_map.set_attribute("level_by_action", level_by_action)
+
+arguments = {
+    "colour_by_action_name": colour_by_action_name,
+}
+
+_, axes = plt.subplots(layout="constrained")
+init_axes(axes)
+plot_bars(axes, pathway_map, arguments=arguments)
+plt.show()

documentation/use/example/ex_15_bar_plot/10_plot_diverging_bar_plot.py

@@ -0,0 +1,58 @@
+"""
+Pathway map for diverging pathways
+==================================
+"""
+
+from io import StringIO
+
+import matplotlib.pyplot as plt
+
+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,
+    plot_bars,
+)
+
+
+actions, colour_by_action = text.read_actions(
+    StringIO(
+        """
+current #ff4c566a
+a #ffbf616a
+b #ffd08770
+c #ffebcb8b
+"""
+    )
+)
+sequences, tipping_point_by_action = text.read_sequences(
+    StringIO(
+        """
+current current 2030
+current a 2040
+current b 2050
+current c 2060
+"""
+    ),
+    actions,
+)
+sequence_graph = SequenceGraph(sequences)
+pathway_map = sequence_graph_to_pathway_map(sequence_graph)
+
+level_by_action = action_level_by_first_occurrence(sequences)
+colour_by_action_name = {
+    action.name: colour for action, colour in colour_by_action.items()
+}
+
+pathway_map.assign_tipping_points(tipping_point_by_action)
+pathway_map.set_attribute("level_by_action", level_by_action)
+
+arguments = {
+    "colour_by_action_name": colour_by_action_name,
+}
+
+_, axes = plt.subplots(layout="constrained")
+init_axes(axes)
+plot_bars(axes, pathway_map, arguments=arguments)
+plt.show()

documentation/use/example/ex_15_bar_plot/15_plot_converging_bar_plot.py

@@ -0,0 +1,62 @@
+"""
+Pathway map for converging pathways
+===================================
+"""
+
+from io import StringIO
+
+import matplotlib.pyplot as plt
+
+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,
+    plot_bars,
+)
+
+
+actions, colour_by_action = text.read_actions(
+    StringIO(
+        """
+current #ff4c566a
+a #ffbf616a
+b #ffd08770
+c #ffebcb8b
+d #ffa3be8c
+"""
+    )
+)
+sequences, tipping_point_by_action = text.read_sequences(
+    StringIO(
+        """
+current current 2030
+current a 2040
+current b 2050
+current c 2060
+a d[1] 2070
+b d[2] 2070
+c d[3] 2070
+"""
+    ),
+    actions,
+)
+sequence_graph = SequenceGraph(sequences)
+pathway_map = sequence_graph_to_pathway_map(sequence_graph)
+
+level_by_action = action_level_by_first_occurrence(sequences)
+colour_by_action_name = {
+    action.name: colour for action, colour in colour_by_action.items()
+}
+
+pathway_map.assign_tipping_points(tipping_point_by_action)
+pathway_map.set_attribute("level_by_action", level_by_action)
+
+arguments = {
+    "colour_by_action_name": colour_by_action_name,
+}
+
+_, axes = plt.subplots(layout="constrained")
+init_axes(axes)
+plot_bars(axes, pathway_map, arguments=arguments)
+plt.show()

documentation/use/example/ex_15_bar_plot/20_plot_example_bar_plot.py

@@ -0,0 +1,69 @@
+"""
+Pathway map for an example
+==========================
+"""
+
+from io import StringIO
+
+import matplotlib.pyplot as plt
+
+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,
+    plot_bars,
+)
+
+
+actions, colour_by_action = text.read_actions(
+    StringIO(
+        """
+current #ff4c566a
+a #ffbf616a
+b #ffd08770
+c #ffebcb8b
+d #ffa3be8c
+e #ffb48ead
+f #ff5e81ac
+"""
+    )
+)
+sequences, tipping_point_by_action = text.read_sequences(
+    StringIO(
+        """
+current     current 2030
+current     a       2040
+a           e[1]    2090
+current     b       2050
+b           f[1]    2080
+current     c       2060
+c           f[2]    2080
+current     d       2070
+d           f[3]    2080
+f[1]        e[2]    2090
+f[2]        e[3]    2090
+f[3]        e[4]    2090
+"""
+    ),
+    actions,
+)
+sequence_graph = SequenceGraph(sequences)
+pathway_map = sequence_graph_to_pathway_map(sequence_graph)
+
+level_by_action = action_level_by_first_occurrence(sequences)
+colour_by_action_name = {
+    action.name: colour for action, colour in colour_by_action.items()
+}
+
+pathway_map.assign_tipping_points(tipping_point_by_action)
+pathway_map.set_attribute("level_by_action", level_by_action)
+
+arguments = {
+    "colour_by_action_name": colour_by_action_name,
+}
+
+_, axes = plt.subplots(layout="constrained")
+init_axes(axes)
+plot_bars(axes, pathway_map, arguments=arguments)
+plt.show()

documentation/use/example/ex_15_bar_plot/25_plot_example_bar_plot.py

@@ -0,0 +1,75 @@
+"""
+Pathway map for an example
+==========================
+"""
+
+from io import StringIO
+
+import matplotlib.pyplot as plt
+
+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,
+    plot_bars,
+)
+
+
+actions, colour_by_action = text.read_actions(
+    StringIO(
+        """
+current #ff4c566a
+a #ffbf616a
+b #ffd08770
+c #ffebcb8b
+d #ffa3be8c
+"""
+    )
+)
+sequences, tipping_point_by_action = text.read_sequences(
+    StringIO(
+        """
+current     current     2030
+
+current     a[1]        2100
+
+current     b[1]        2040
+b[1]        a[2]        2100
+b[1]        c[2]        2050
+c[2]        b[2]        2070
+b[2]        a[3]        2100
+c[2]        a[4]        2100
+c[2]        d[3]        2100
+b[1]        d[2]        2100
+
+current     c[1]        2050
+c[1]        b[3]        2070
+b[3]        a[5]        2100
+c[1]        a[6]        2100
+c[1]        d[4]        2100
+
+current     d[1]        2100
+"""
+    ),
+    actions,
+)
+sequence_graph = SequenceGraph(sequences)
+pathway_map = sequence_graph_to_pathway_map(sequence_graph)
+
+level_by_action = action_level_by_first_occurrence(sequences)
+colour_by_action_name = {
+    action.name: colour for action, colour in colour_by_action.items()
+}
+
+pathway_map.assign_tipping_points(tipping_point_by_action)
+pathway_map.set_attribute("level_by_action", level_by_action)
+
+arguments = {
+    "colour_by_action_name": colour_by_action_name,
+}
+
+_, axes = plt.subplots(layout="constrained")
+init_axes(axes)
+plot_bars(axes, pathway_map, arguments=arguments)
+plt.show()

documentation/use/example/ex_15_bar_plot/README.rst

@@ -0,0 +1,2 @@
+Examples of bar plots
+=====================

documentation/use/plot.rst

@@ -7,10 +7,12 @@ Plotting pathways
    Examples <example/index>
 
 
-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.pathway_map.plot.PathwayMapLayout.CLASSIC>` layout.
+The package contains multiple command-line applications.
+``ap_plot_graphs`` and can be used to gain insight into various kinds of graphs used to store information
+about pathways.
+``ap_plot_pathway_map`` can be used to visualize pathway maps in the so-called
+:const:`CLASSIC <adaptation_pathways.plot.pathway_map.plot.PathwayMapLayout.CLASSIC>` layout.
+``ap_plot_bars`` can be used to visualize pathways using bar plots.
 
 
 ``ap_plot_graphs``
@@ -54,3 +56,22 @@ Example for creating a plot from ``my_pathways-action.txt`` and ``my_pathways-se
    ap_plot_pathway_map my_pathways my_pathways.pdf
 
 For help about the usage of the command type ``ap_plot_pathway_map --help``.
+
+
+``ap_plot_bars``
+----------------
+See also:
+:mod:`adaptation_pathways.cli.plot_bars`,
+:class:`PathwayMap <adaptation_pathways.graph.pathway_map.PathwayMap>`
+
+This command takes information about pathways as input, and outputs a single plot containing
+the pathways visualized by horizontal bars.
+
+Example for creating a plot from ``my_pathways-action.txt`` and ``my_pathways-sequence.txt``
+(or ``my_pathways.apw``) to ``./my_pathways.pdf``:
+
+.. code-block:: bash
+
+   ap_plot_bars my_pathways my_pathways.pdf
+
+For help about the usage of the command type ``ap_plot_bars --help``.

pyproject.toml

@@ -45,6 +45,7 @@ dependencies = [
 [project.scripts]
 ap_export = "adaptation_pathways.cli.export:main"
 ap_import = "adaptation_pathways.cli.import_:main"
+ap_plot_bars = "adaptation_pathways.cli.plot_bars:main"
 ap_plot_graphs = "adaptation_pathways.cli.plot_graphs:main"
 ap_plot_pathway_map = "adaptation_pathways.cli.plot_pathway_map:main"