From eecdc9ae5b0d5e7a590611bafb036487c0433277 Mon Sep 17 00:00:00 2001 From: Leonardo Schwarz Date: Fri, 7 Jun 2024 17:39:17 +0200 Subject: [PATCH] add rules for mini plot --- .../workflow/experimental.smk | 39 ++++++++++++++++++- 1 file changed, 38 insertions(+), 1 deletion(-) diff --git a/src/depiction_targeted_preproc/workflow/experimental.smk b/src/depiction_targeted_preproc/workflow/experimental.smk index fb22d3b..e816401 100644 --- a/src/depiction_targeted_preproc/workflow/experimental.smk +++ b/src/depiction_targeted_preproc/workflow/experimental.smk @@ -44,4 +44,41 @@ rule exp_plot_compare_peak_density: "python -m depiction_targeted_preproc.workflow.exp.plot_compare_peak_density" " {input.tables_marker_distance}" " --table-marker-distance-uncalib {input.table_marker_distance_uncalib}" - " --output-pdf {output.pdf}" \ No newline at end of file + " --output-pdf {output.pdf}" + + +# for the poster: +rule qc_table_marker_distances_baseline_mini: + input: + imzml=multiext("{sample}/corrected.peaks",".imzML",".ibd"), + mass_list="{sample}/mass_list.visualization_mini.csv", + output: + table="{sample}/qc/table_marker_distances_baseline_mini.parquet" + shell: + "python -m depiction_targeted_preproc.workflow.qc.table_marker_distances" + " --imzml-peaks {input.imzml[0]} --mass-list {input.mass_list}" + " --output-table {output.table}" + +rule qc_table_marker_distances_calib_mini: + input: + imzml_peaks="{sample}/calibrated.imzML", + mass_list="{sample}/mass_list.visualization_mini.csv", + output: + table="{sample}/qc/table_marker_distances_calib_mini.parquet" + shell: + "python -m depiction_targeted_preproc.workflow.qc.table_marker_distances" + " --imzml-peaks {input.imzml_peaks} --mass-list {input.mass_list}" + " --output-table {output.table}" + +rule qc_plot_marker_presence_mini: + input: + table_marker_distances_baseline="{sample}/qc/table_marker_distances_baseline_mini.parquet", + table_marker_distances_calib="{sample}/qc/table_marker_distances_calib_mini.parquet" + output: + pdf="{sample}/qc/plot_marker_presence.pdf" + shell: + "python -m depiction_targeted_preproc.workflow.qc.plot_marker_presence" + " --table-marker-distances-baseline {input.table_marker_distances_baseline}" + " --table-marker-distances-calib {input.table_marker_distances_calib}" + " --output-pdf {output.pdf}" +