rename the old plot too

fgcz · Jun 28, 2024 · 877e483 · 877e483
1 parent 7f56bdb
commit 877e483
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Showing 4 changed files with 8 additions and 8 deletions.
diff --git a/src/depiction_targeted_preproc/pipeline_config/artifacts_mapping.py b/src/depiction_targeted_preproc/pipeline_config/artifacts_mapping.py
@@ -10,6 +10,7 @@
         "qc/plot_marker_presence.pdf",
         "qc/plot_peak_density_combined.pdf",
         "qc/plot_peak_density_grouped.pdf",
+        "qc/plot_peak_counts_per_spectrum.pdf",
         "qc/plot_peak_counts_per_mass_range.pdf",
         "qc/plot_scan_direction.pdf",
     ],
@@ -24,7 +25,6 @@
         "qc/plot_marker_presence_cv.pdf",
         # "qc/plot_spectra_for_marker.pdf",
         # "qc/plot_sample_spectra_before_after.pdf",
-        "qc/plot_peak_counts.pdf",
         "cluster_default_kmeans.hdf5",
         #        "cluster_default_stats_kmeans.csv",
         "cluster_default_kmeans.png",

diff --git a/src/depiction_targeted_preproc/workflow/qc/plot_peak_counts_per_mass_range.py b/src/depiction_targeted_preproc/workflow/qc/plot_peak_counts_per_mass_range.py
@@ -10,7 +10,7 @@
 from depiction.persistence import ImzmlReadFile
 from depiction_targeted_preproc.pipeline_config.model import PipelineParameters
 from depiction_targeted_preproc.workflow.qc.plot_calibration_map import get_mass_groups
-from depiction_targeted_preproc.workflow.qc.plot_peak_counts import get_peak_counts
+from depiction_targeted_preproc.workflow.qc.plot_peak_counts_per_spectrum import get_peak_counts
 
 
 def qc_plot_peak_counts_per_mass_range(

diff --git a/...d_preproc/workflow/qc/plot_peak_counts.py → ...kflow/qc/plot_peak_counts_per_spectrum.py b/...d_preproc/workflow/qc/plot_peak_counts.py → ...kflow/qc/plot_peak_counts_per_spectrum.py
@@ -11,7 +11,7 @@
 
 
 def get_peak_counts(read_peaks: ImzmlReadFile, mass_groups: pl.DataFrame, n_jobs: int) -> pl.DataFrame:
-    # TODO parallelize, over all
+    # TODO parallelize, over all !!!FIXME
     collect = []
     with read_peaks.reader() as reader:
         for i_spectrum in range(1000):
@@ -26,7 +26,7 @@ def get_peak_counts(read_peaks: ImzmlReadFile, mass_groups: pl.DataFrame, n_jobs
     return pl.DataFrame(collect)
 
 
-def qc_plot_peak_counts(
+def qc_plot_peak_counts_per_spectrum(
     imzml_peaks: Annotated[Path, Option()],
     output_pdf: Annotated[Path, Option()],
     config_path: Annotated[Path, Option()],
@@ -49,4 +49,4 @@ def qc_plot_peak_counts(
 
 
 if __name__ == "__main__":
-    typer.run(qc_plot_peak_counts)
+    typer.run(qc_plot_peak_counts_per_spectrum)
diff --git a/src/depiction_targeted_preproc/workflow/rules/rules_qc.smk b/src/depiction_targeted_preproc/workflow/rules/rules_qc.smk
@@ -127,14 +127,14 @@ rule qc_plot_spectra_for_marker:
         " --output-pdf {output.pdf}"
 
 
-rule qc_plot_peak_counts:
+rule qc_plot_peak_counts_per_spectrum:
     input:
         imzml=multiext("{sample}/corrected.peaks", ".imzML", ".ibd"),
         config="{sample}/pipeline_params.yml",
     output:
-        pdf="{sample}/qc/plot_peak_counts.pdf",
+        pdf="{sample}/qc/plot_peak_counts_per_spectrum.pdf",
     shell:
-        "python -m depiction_targeted_preproc.workflow.qc.plot_peak_counts"
+        "python -m depiction_targeted_preproc.workflow.qc.plot_peak_counts_per_spectrum"
         " --config-path {input.config} --imzml-peaks {input.imzml[0]}"
         " --output-pdf {output.pdf}"