Merge pull request #48 from geoneric/gh40

Replace current function by a custom plotting function

documentation/use/example/ex_10_pathway_map/05_plot_serial_pathway_map_classic.py

@@ -49,7 +49,11 @@
 pathway_map.set_attribute("level_by_action", level_by_action)
 pathway_map.set_attribute("colour_by_action_name", colour_by_action_name)
 
+arguments = {
+    "colour_by_action_name": colour_by_action_name,
+}
+
 _, axes = plt.subplots(layout="constrained")
 init_axes(axes)
-plot_classic_pathway_map(axes, pathway_map)
+plot_classic_pathway_map(axes, pathway_map, arguments=arguments)
 plt.show()

documentation/use/example/ex_10_pathway_map/10_plot_diverging_pathway_map_classic.py

@@ -49,7 +49,11 @@
 pathway_map.set_attribute("level_by_action", level_by_action)
 pathway_map.set_attribute("colour_by_action_name", colour_by_action_name)
 
+arguments = {
+    "colour_by_action_name": colour_by_action_name,
+}
+
 _, axes = plt.subplots(layout="constrained")
 init_axes(axes)
-plot_classic_pathway_map(axes, pathway_map)
+plot_classic_pathway_map(axes, pathway_map, arguments=arguments)
 plt.show()

documentation/use/example/ex_10_pathway_map/15_plot_converging_pathway_map_classic.py

@@ -53,7 +53,11 @@
 pathway_map.set_attribute("level_by_action", level_by_action)
 pathway_map.set_attribute("colour_by_action_name", colour_by_action_name)
 
+arguments = {
+    "colour_by_action_name": colour_by_action_name,
+}
+
 _, axes = plt.subplots(layout="constrained")
 init_axes(axes)
-plot_classic_pathway_map(axes, pathway_map)
+plot_classic_pathway_map(axes, pathway_map, arguments=arguments)
 plt.show()

documentation/use/example/ex_10_pathway_map/20_plot_example_pathway_map_classic.py

@@ -60,7 +60,11 @@
 pathway_map.set_attribute("level_by_action", level_by_action)
 pathway_map.set_attribute("colour_by_action_name", colour_by_action_name)
 
+arguments = {
+    "colour_by_action_name": colour_by_action_name,
+}
+
 _, axes = plt.subplots(layout="constrained")
 init_axes(axes)
-plot_classic_pathway_map(axes, pathway_map)
+plot_classic_pathway_map(axes, pathway_map, arguments=arguments)
 plt.show()

documentation/use/example/ex_10_pathway_map/25_plot_example_pathway_map_classic.py

@@ -66,7 +66,11 @@
 pathway_map.set_attribute("level_by_action", level_by_action)
 pathway_map.set_attribute("colour_by_action_name", colour_by_action_name)
 
+arguments = {
+    "colour_by_action_name": colour_by_action_name,
+}
+
 _, axes = plt.subplots(layout="constrained")
 init_axes(axes)
-plot_classic_pathway_map(axes, pathway_map)
+plot_classic_pathway_map(axes, pathway_map, arguments=arguments)
 plt.show()

pyproject.toml

@@ -6,6 +6,7 @@ profile = "black"
 
 [tool.pylint]
 disable = "C0103, C0114, C0115, C0116, C0302, E0401, W0212, W0511, R0801"
+max-line-length=240
 extension-pkg-allow-list = [
     "matplotlib",
     "PySide6",

source/package/adaptation_pathways/cli/plot_pathway_map.py

@@ -1,5 +1,6 @@
 import os.path
 import sys
+import typing
 
 import docopt
 import matplotlib.pyplot as plt
@@ -13,10 +14,15 @@
 
 
 @main_function
-def plot_map(basename_pathname: str, plot_pathname: str) -> int:
+def plot_map(
+    basename_pathname: str,
+    plot_pathname: str,
+    *,
+    arguments,
+) -> int:
 
     # pylint: disable-next=unused-variable
-    actions, sequences, tipping_point_by_action, colour_by_action = read_dataset(
+    _, sequences, tipping_point_by_action, colour_by_action = read_dataset(
         basename_pathname
     )
 
@@ -35,7 +41,11 @@ def plot_map(basename_pathname: str, plot_pathname: str) -> int:
 
     _, axes = plt.subplots(layout="constrained")
     init_axes(axes)
-    plot_classic_pathway_map(axes, pathway_map, title="Pathway map")
+
+    # TODO This should be colour_by_action
+    arguments["colour_by_action_name"] = colour_by_action_name
+
+    plot_classic_pathway_map(axes, pathway_map, arguments=arguments)
     save_plot(plot_pathname)
 
     return 0
@@ -47,7 +57,8 @@ def main() -> int:
 Plot pathway map
 
 Usage:
-    {command} <basename> <plot>
+    {command} [--title=<title>] [--x_label=<label>] [--show_legend]
+        [--overshoot] <basename> <plot>
 
 Arguments:
     basename           Either, the name without postfix and extension of text
@@ -60,6 +71,11 @@ def main() -> int:
 Options:
     -h --help          Show this screen and exit
     --version          Show version and exit
+    --overshoot        Show tipping points as overshoots, extending a little
+                       bit beyond the actual point
+    --show_legend      Show legend
+    --title=<title>    Title
+    --x_label=<label>  Label of x-axis
 
 The format for storing sequences is simple: per line mention the names of
 two actions that form a sequence. Information from multiple lines can result
@@ -70,12 +86,24 @@ def main() -> int:
     {command} serial serial.pdf
     {command} serial.apw serial.pdf
 """
-    arguments = sys.argv[1:]
-    arguments = docopt.docopt(usage, arguments, version=version)
-    basename_pathname = arguments["<basename>"]  # type: ignore
-    plot_pathname = arguments["<plot>"]  # type: ignore
+    arguments = docopt.docopt(usage, sys.argv[1:], version=version)
+    basename_pathname = arguments["<basename>"]
+    plot_pathname = arguments["<plot>"]
+    title = arguments["--title"] if arguments["--title"] is not None else ""
+    x_label = arguments["--x_label"] if arguments["--x_label"] is not None else ""
+    show_legend = arguments["--show_legend"]
+    overshoot = arguments["--overshoot"]
+
+    plot_arguments: dict[str, typing.Any] = {
+        "title": title,
+        "x_label": x_label,
+        "show_legend": show_legend,
+    }
+
+    if overshoot:
+        plot_arguments["tipping_point_overshoot"] = 0.4
 
     if len(os.path.splitext(plot_pathname)[1]) == 0:
         plot_pathname += ".pdf"
 
-    return plot_map(basename_pathname, plot_pathname)
+    return plot_map(basename_pathname, plot_pathname, arguments=plot_arguments)

source/package/adaptation_pathways/desktop/application.py

@@ -23,9 +23,7 @@
 from ..plot import (
     pathway_graph_node_colours,
     pathway_map_edge_colours,
-    pathway_map_edge_styles,
     pathway_map_node_colours,
-    pathway_map_node_styles,
     plot_classic_pathway_map,
     plot_default_pathway_graph,
     plot_default_pathway_map,
@@ -288,15 +286,6 @@ def _plot_pathway_map(self, pathway_map: PathwayMap) -> None:
         self.pathway_map_widget.draw()
 
     def _plot_pathway_classic_map(self, pathway_map: PathwayMap) -> None:
-        plot_colours = PlotColours(
-            pathway_map_node_colours(pathway_map, self.colour_by_action_name),
-            pathway_map_node_styles(pathway_map),
-            pathway_map_edge_colours(pathway_map, self.colour_by_action_name),
-            pathway_map_edge_styles(pathway_map),
-            default_node_edge_colours(pathway_map),
-            default_label_colour(),
-        )
-
         if pathway_map.nr_nodes() > 0:
             pathway_map.assign_tipping_points(self.tipping_point_by_action, verify=True)
 
@@ -306,9 +295,11 @@ def _plot_pathway_classic_map(self, pathway_map: PathwayMap) -> None:
         pathway_map.set_attribute("level_by_action", level_by_action)
         pathway_map.set_attribute("colour_by_action_name", self.colour_by_action_name)
 
+        arguments = {"colour_by_action_name": self.colour_by_action_name}
+
         self.pathway_map_classic_widget.axes.clear()
         plot_classic_pathway_map(
-            self.pathway_map_classic_widget.axes, pathway_map, plot_colours=plot_colours
+            self.pathway_map_classic_widget.axes, pathway_map, arguments=arguments
         )
         self.pathway_map_classic_widget.draw()