Number workflows

nuc_morph_analysis/analyses/inhibitors/run_all_inhibitor_analysis_workflow.py → nuc_morph_analysis/analyses/inhibitors/figure_s6_s16_workflow.py

@@ -15,3 +15,5 @@ def run_inhibitor_work():
 _ = global_dataset_filtering.load_dataset_with_features("all_drug_perturbation", save_local=True)
 
 run_inhibitor_work()
+
+# %%

nuc_morph_analysis/analyses/volume/trajectories_workflow.py → nuc_morph_analysis/analyses/volume/figure_4_s8_workflow.py

@@ -21,13 +21,13 @@
 df_full = filter_data.all_timepoints_full_tracks(df)
 df_track_level_features = filter_data.track_level_features(df_full)
 
+# %% MAIN FIGURE PANELS
+
 # %%
 # Plot all tracks all datasets synchronized in real or normalized time
 for time in ["sync_time_Ff", "normalized_time"]:
     plot_tracks.plot_all_tracks_synchronized(df_full, figdir, "volume", time)
 
-# %% MAIN FIGURE PANELS
-
 # %%
 # Plot single sample track from same nucleus as in formation/breakdown figure
 

nuc_morph_analysis/analyses/volume/local_growth_workflow.py → nuc_morph_analysis/analyses/volume/figure_5_s9_workflow.py

@@ -234,3 +234,5 @@
             add_unity_line=True,
             remove_all_points_in_pdf=pngflag,
         )
+
+# %%

nuc_morph_analysis/lib/preprocessing/filter_data.py

@@ -939,6 +939,7 @@ def all_timepoints_full_tracks(df):
     """
     df = all_timepoints_minimal_filtering(df)
     df = df.loc[df["is_full_track"] == True]
+    df = df.sort_values('index_sequence')
     return df
 
 

run_all_manuscript_workflows.py

@@ -1,68 +1,66 @@
 import argparse
 from nuc_morph_analysis.utilities.workflow_runner import get_jobs, execute
 from nuc_morph_analysis.analyses.colony_area import colony_area_workflow
+from nuc_morph_analysis.analyses.segmentation_model_validation import seg_model_validation_figure_workflow
 
 
 class Workflows:
-    def figure1_dataset():
-        import nuc_morph_analysis.analyses.dataset_images_for_figures.run_all_figure_1_code
-
+    def figure_1_dataset():
+        import nuc_morph_analysis.analyses.dataset_images_for_figures.figure_1_workflow
         # panel E items are generated in segmentation_model_validation
-
-    def figure1_main_text():
         colony_area_workflow.baseline_colony_starting_area()
-
-    def figure3_figureS2_height():
-        import nuc_morph_analysis.analyses.height.height_workflow
-
-    def figure4_figureS5_volume_trajectories():
-        # excludes aphidicolin panel S5C
-        import nuc_morph_analysis.analyses.volume.trajectories_workflow
-
-    def figure5_figureS6_local_growth():
-        import nuc_morph_analysis.analyses.volume.local_growth_workflow
-
-    def figure6_figureS7_compensation():
-        import nuc_morph_analysis.analyses.volume_variation.compensation_workflow
-
-    def figure7_lineage():
-        import nuc_morph_analysis.analyses.lineage.lineage_manuscript_workflow
-
-    def figure_inhibitors():
-        import nuc_morph_analysis.analyses.inhibitors.run_all_inhibitor_analysis_workflow
-
+
+    def figure_s1_cell_health():
+        import nuc_morph_analysis.analyses.cell_health.figure_s1_workflow
+
+    def figure_s2_s3_s18_segmentation_model_validation():
+        seg_model_validation_figure_workflow.save_out_specified_image_pairs_with_overlays()
+        import nuc_morph_analysis.analyses.segmentation_model_validation.quantitative_validation_workflow
+
+    # figure 2 images generated using timelapse feature exploroer   
+
+    def figure_3_s4_height_density():
+        # figure 3 images generated using timelapse feauture explorer
+        import nuc_morph_analysis.analyses.height.figure_3_s4_workflow
+
+    # figure s5 image data can be found on quilt
+
+    def figure_s6_s16_inhibitors():
+        import nuc_morph_analysis.analyses.inhibitors.figure_s6_s16_workflow
         colony_area_workflow.aphidicolin_control_starting_area()
         colony_area_workflow.importazole_control_starting_area()
+
+    def figure_s7_growth_outliers():
+        import nuc_morph_analysis.analyses.evaluate_filters_and_outliers.figure_s7_workflow
+
+    def figure_4_s8_volume_trajectories():
+        import nuc_morph_analysis.analyses.volume.figure_4_s8_workflow
+
+    def figure_5_s9_local_growth():
+        import nuc_morph_analysis.analyses.volume.figure_5_s9_workflow
+        #s10 coming soon
 
-    def transition_point():
-        import nuc_morph_analysis.analyses.volume.supplement_vis_transition_point_calculation_workflow
-
-    def growth_outliers():
-        import nuc_morph_analysis.analyses.evaluate_filters_and_outliers.growth_feature_outliers_workflow
-
-    def error():
-        import nuc_morph_analysis.analyses.error_morflowgenesis.workflows.fixed_control_analysis_manuscript_workflow
-
-    def feeding_control():
-        import nuc_morph_analysis.analyses.feeding_control.feeding_control_manuscript_workflow
-
+    def figure_6_s11_compensation():
+        import nuc_morph_analysis.analyses.volume_variation.figure_6_s11_workflow
+
+    def figure_s12_feeding_control():
+        import nuc_morph_analysis.analyses.feeding_control.figure_s12_workflow
         colony_area_workflow.feeding_control_starting_area()
 
-    def figureS1_segmentation_model_validation():
-        from nuc_morph_analysis.analyses.segmentation_model_validation import (
-            seg_model_validation_figure_workflow,
-        )
+    def figure_7_s13_s14_lineage():
+        import nuc_morph_analysis.analyses.lineage.figure_7_s13_s14_workflow
 
-        seg_model_validation_figure_workflow.save_out_specified_image_pairs_with_overlays()
-        import nuc_morph_analysis.analyses.segmentation_model_validation.quantitative_validation_workflow
+    def figure_s15_linear_regression_model():
+        import nuc_morph_analysis.analyses.linear_regression.figure_s15_workflow
+
+    # figure s17 image data can be found on quilt
+
+    def figure_s19_transition_point():
+        import nuc_morph_analysis.analyses.volume.figure_s19_workflow
 
-    def supplemental_figure_cell_health():
-        import nuc_morph_analysis.analyses.cell_health.cell_health_workflow
-
-    def supplemental_figure_linear_regression_model():
-        import nuc_morph_analysis.analyses.linear_regression.supplemental_lrm_figure_workflow
-
-
+    def figure_s20_precision_error():
+        import nuc_morph_analysis.analyses.error_morflowgenesis.workflows.figure_s20_workflow
+
 ALL_WORKFLOWS = get_jobs(Workflows)
 
 parser = argparse.ArgumentParser(description="Run all manuscript workflows")