Passthrough surface name

kymata-atlas · Mar 8, 2024 · e1ddd2d · e1ddd2d
1 parent 97404fa
commit e1ddd2d
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Showing 2 changed files with 18 additions and 32 deletions.
diff --git a/invokers/invoker_run_nkg_plotting.py b/invokers/invoker_run_nkg_plotting.py
@@ -1,41 +1,26 @@
-from pathlib import Path
 from os import path
+from pathlib import Path
 
+from kymata.datasets.sample import KymataMirror2023Q3Dataset
 from kymata.io.config import load_config
-from kymata.io.nkg import load_expression_set
 from kymata.plot.plot import expression_plot
 
+
 # template invoker for printing out expression set .nkgs
 def main():
     config = load_config(str(Path(Path(__file__).parent.parent, "kymata", "config", "dataset4.yaml")))
 
-    path_to_nkg_files = Path(Path(path.abspath("")).parent, "kymata-toolbox-data", "output")
-
-    expression_data = load_expression_set(Path( path_to_nkg_files, "IL_gridsearch.nkg"))
-    expression_data += load_expression_set(Path( path_to_nkg_files, "STL_gridsearch.nkg"))
-    expression_data += load_expression_set(Path( path_to_nkg_files, "IL1_gridsearch.nkg"))
-    expression_data += load_expression_set(Path( path_to_nkg_files, "IL2_gridsearch.nkg"))
-    expression_data += load_expression_set(Path( path_to_nkg_files, "IL3_gridsearch.nkg"))
-    expression_data += load_expression_set(Path( path_to_nkg_files, "IL4_gridsearch.nkg"))
-    expression_data += load_expression_set(Path( path_to_nkg_files, "IL5_gridsearch.nkg"))
-    expression_data += load_expression_set(Path( path_to_nkg_files, "IL6_gridsearch.nkg"))
-    expression_data += load_expression_set(Path( path_to_nkg_files, "IL7_gridsearch.nkg"))
-    expression_data += load_expression_set(Path( path_to_nkg_files, "IL8_gridsearch.nkg"))
-    expression_data += load_expression_set(Path( path_to_nkg_files, "IL9_gridsearch.nkg"))
+    expression_data = KymataMirror2023Q3Dataset().to_expressionset()
 
     expression_plot(expression_data,
-                    color = {
-                        'IL': '#b11e34',
-                        'IL1': '#a201e9',
-                        'IL2': '#a201e9',
-                        'IL3': '#a201e9',
-                        'IL4': '#a201e9',
-                        'IL5': '#a201e9',
-                        'IL6': '#a201e9',
-                        'IL7': '#a201e9',
-                        'IL8': '#a201e9',
-                        'IL9': '#a201e9',
-                        'STL': '#d388b5'
-                        },
+                    show_only=[
+                        'CIECAM02 A',
+                        'CIECAM02 a',
+                    ],
                     minimap_config=config,
-                    )
+                    minimap_view="caudal",
+                    minimap_surface="inflated",
+                    )
+
+if __name__ == '__main__':
+    main()
diff --git a/kymata/plot/plot.py b/kymata/plot/plot.py
@@ -184,7 +184,7 @@ def _plot_minimap_sensor(expression_set: ExpressionSet, minimap_axis: pyplot.Axe
 def _plot_minimap_hexel(expression_set: HexelExpressionSet,
                         show_functions: list[str],
                         lh_minimap_axis: pyplot.Axes, rh_minimap_axis: pyplot.Axes,
-                        view: str,
+                        view: str, surface: str,
                         colors: dict[str, Any], alpha_logp: float):
     transparent = (0, 0, 0, 0)
 
@@ -209,7 +209,7 @@ def _plot_minimap_hexel(expression_set: HexelExpressionSet,
     warn("Plotting on the fsaverage brain. Ensure that hexel numbers match those of the fsaverage brain.")
     plot_kwargs = dict(
         subject='fsaverage',
-        surface="inflated",
+        surface=surface,
         views=view,
         colormap=colormap,
         smoothing_steps=1,
@@ -254,6 +254,7 @@ def expression_plot(
         # Display options
         minimap_config: Optional[dict[str, str]] = None,
         minimap_view: str = "lateral",
+        minimap_surface: str = "inflated",
         # I/O args
         save_to: Optional[Path] = None,
         overwrite: bool = True,
@@ -432,7 +433,7 @@ def expression_plot(
                                 show_functions=show_only,
                                 lh_minimap_axis=axes[_AxName.minimap_top],
                                 rh_minimap_axis=axes[_AxName.minimap_bottom],
-                                view=minimap_view,
+                                view=minimap_view, surface=minimap_surface,
                                 colors=color, alpha_logp=sidak_corrected_alpha)
         else:
             raise NotImplementedError()