add mini variant

fgcz · Jun 7, 2024 · 8d0600d · 8d0600d
1 parent c4543e9
commit 8d0600d
Show file tree

Hide file tree

Showing 2 changed files with 9 additions and 1 deletion.
diff --git a/src/depiction_targeted_preproc/workflow/exp/mass_list_preparation.py b/src/depiction_targeted_preproc/workflow/exp/mass_list_preparation.py
@@ -11,6 +11,7 @@ def exp_mass_list_preparation(
     out_calibration_csv_path: Annotated[Path, Option()],
     out_standards_csv_path: Annotated[Path, Option()],
     out_visualization_csv_path: Annotated[Path, Option()],
+    out_visualization_mini_csv_path: Annotated[Path, Option()] = None,
 ) -> None:
     input_df = pl.read_csv(input_csv_path)
 
@@ -31,6 +32,11 @@ def exp_mass_list_preparation(
     standards_df.write_csv(out_standards_csv_path)
     visualization_df.write_csv(out_visualization_csv_path)
 
+    if out_visualization_mini_csv_path:
+        choices = ["Angiotensin standard", "CD38", "CD20", "Caveolin-1", "VIM", "CD36", "FN1", "Ki67"]
+        visualization_mini_df = visualization_df.filter(pl.col("label").is_in(choices))
+        visualization_mini_df.write_csv(out_visualization_mini_csv_path)
+
 
 if __name__ == "__main__":
     typer.run(exp_mass_list_preparation)
diff --git a/src/depiction_targeted_preproc/workflow/experimental.smk b/src/depiction_targeted_preproc/workflow/experimental.smk
@@ -23,13 +23,15 @@ rule exp_mass_list_preparation:
     output:
         calibration_csv="{sample}/mass_list.calibration.csv",
         standards_csv="{sample}/mass_list.standards.csv",
-        visualization_csv="{sample}/mass_list.visualization.csv"
+        visualization_csv="{sample}/mass_list.visualization.csv",
+        visualization_mini_csv="{sample}/mass_list.visualization_mini.csv"
     shell:
         "python -m depiction_targeted_preproc.workflow.exp.mass_list_preparation"
         " --input-csv-path {input.csv}"
         " --out-calibration-csv-path {output.calibration_csv}"
         " --out-standards-csv-path {output.standards_csv}"
         " --out-visualization-csv-path {output.visualization_csv}"
+        " --out-visualization-mini-csv-path {output.visualization_mini_csv}"
 
 
 rule exp_plot_compare_peak_density: