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sreichlsreichl
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refactorize docs/wiki plots
1 parent 661d623 commit 5575551

5 files changed

Lines changed: 125 additions & 121 deletions

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‎workflow/Snakefile‎

Lines changed: 5 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -36,6 +36,7 @@ for ds in config["workflows"]:
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include: os.path.join("rules", "CorcesRNA.smk")
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include: os.path.join("rules", "CorcesATAC.smk")
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include: os.path.join("rules", "CorcesINT.smk")
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include: os.path.join("rules", "docs.smk")
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#### Target Rule ####
@@ -54,7 +55,6 @@ rule all:
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rules.CorcesRNA_dea_limma_all.input,
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rules.CorcesRNA_enrichment_analysis_all.input,
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rules.CorcesRNA_reconstruct_lineage.output, # custom rule
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rules.CorcesRNA_plots.output, # custom rule; use only for docs; commented
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#### ATAC-seq Analysis Recipe (CorcesATAC) ####
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rules.CorcesATAC_fetch_ngs_all.input,
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rules.CorcesATAC_get_resources.output, # custom rule
@@ -65,14 +65,16 @@ rule all:
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rules.CorcesATAC_dea_limma_all.input,
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rules.CorcesATAC_enrichment_analysis_all.input,
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rules.CorcesATAC_reconstruct_lineage.output, # custom rule
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rules.CorcesATAC_plots.output, # custom rule; use only for docs; commented
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#### Integrative Analysis Recipe (CorcesINT) ####
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rules.CorcesINT_spilterlize_integrate_all.input,
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rules.CorcesINT_unsupervised_analysis_all.input,
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rules.CorcesINT_dea_limma_all.input,
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rules.CorcesINT_plot_correlation.output, # custom rule for divergent gene visualization
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rules.CorcesINT_enrichment_analysis_all.input,
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rules.CorcesINT_plots.output, # custom rule; use only for docs; commented
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#### Custom rules used only for docs/wiki (keep commented) ####
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rules.CorcesRNA_plots.output,
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rules.CorcesATAC_plots.output,
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rules.CorcesINT_plots.output,
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default_target: True # important for module usage
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threads: 1
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resources:

‎workflow/rules/CorcesATAC.smk‎

Lines changed: 0 additions & 40 deletions
Original file line numberDiff line numberDiff line change
@@ -140,43 +140,3 @@ rule CorcesATAC_reconstruct_lineage:
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os.path.join("logs","rules","CorcesATAC_reconstruct_lineage.log"),
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script:
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"../scripts/crossprediction.py"
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#### CorcesATAC - Copy selected plots for documentation and visualization in wiki (custom rule) ####
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# Define the mapping of input to output files
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CorcesATAC_plots_map = {
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"sample_annotation.png": "results/CorcesATAC/atacseq_pipeline/report/sample_annotation.png",
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"CD34.svg": "results/CorcesATAC/genome_tracks/tracks/CD34.svg",
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"MS4A1.svg": "results/CorcesATAC/genome_tracks/tracks/MS4A1.svg",
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"filtered.png": "results/CorcesATAC/spilterlize_integrate/all/plots/filtered.png",
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"normCQN_integrated.png": "results/CorcesATAC/spilterlize_integrate/all/plots/normCQN_integrated.png",
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"filtered_CFA.png": "results/CorcesATAC/spilterlize_integrate/all/plots/filtered_CFA.png",
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"normCQN_integrated_CFA.png": "results/CorcesATAC/spilterlize_integrate/all/plots/normCQN_integrated_CFA.png",
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"normCQN_integrated_PCA.png": "results/CorcesATAC/unsupervised_analysis/normCQN_integrated/PCA/plots/PCA_auto_0.9_2/metadata/cell_type.png",
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"normCQN_integrated_HVF_PCA.png": "results/CorcesATAC/unsupervised_analysis/normCQN_integrated_HVF/PCA/plots/PCA_auto_0.9_2/metadata/cell_type.png",
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"normCQN_integrated_UMAP.png": "results/CorcesATAC/unsupervised_analysis/normCQN_integrated/UMAP/plots/UMAP_correlation_15_0.1_2/metadata/cell_type.png",
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"normCQN_integrated_HVF_UMAP.png": "results/CorcesATAC/unsupervised_analysis/normCQN_integrated_HVF/UMAP/plots/UMAP_correlation_15_0.1_2/metadata/cell_type.png",
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"dea_stats.png": "results/CorcesATAC/dea_limma/normCQN_OvA_cell_type/plots/stats.png",
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"markerGenes.png": "results/CorcesATAC/dea_limma/normCQN_OvA_cell_type/plots/heatmap/markerGenes.png",
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"Bcell_up_ReactomePathways.png": "results/CorcesATAC/enrichment_analysis/Bcell_up/GREAT/ReactomePathways/Bcell_up_ReactomePathways.png",
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"Bcell_up_Azimuth_2023.png": "results/CorcesATAC/enrichment_analysis/Bcell_up/GREAT/Azimuth_2023/Bcell_up_Azimuth_2023.png",
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"cell_types_Azimuth_2023_summary.png": "results/CorcesATAC/enrichment_analysis/cell_types_up/GREAT/Azimuth_2023/cell_types_up_Azimuth_2023_summary.png",
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"cell_types_ReactomePathways_summary.png": "results/CorcesATAC/enrichment_analysis/cell_types_up/GREAT/ReactomePathways/cell_types_up_ReactomePathways_summary.png",
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"crossprediction_graph.png": "results/CorcesATAC/special_analyses/crossprediction/graph.png",
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}
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# Copy input to outputs to include the plots in the repo and wiki
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# This rule can only be used for docs after all results (including untracked ones: volcano and unsupervised analysis plots)
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# have been generated (i.e. leave commented in the Snakefile's target rule until the end/last iteration)
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rule CorcesATAC_plots:
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input:
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[CorcesATAC_plots_map[plot] for plot in CorcesATAC_plots_map]
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output:
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[f"docs/CorcesATAC/{plot}" for plot in CorcesATAC_plots_map]
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resources:
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mem_mb="1000",
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threads: config.get("threads", 1)
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log:
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"logs/rules/CorcesATAC_plots.log",
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run:
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for i, o in zip(input, output):
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shell(f"cp {i} {o}")

‎workflow/rules/CorcesINT.smk‎

Lines changed: 0 additions & 38 deletions
Original file line numberDiff line numberDiff line change
@@ -106,41 +106,3 @@ module CorcesINT_enrichment_analysis:
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config_wf["CorcesINT_enrichment_analysis"]
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use rule * from CorcesINT_enrichment_analysis as CorcesINT_enrichment_analysis_*
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#### CorcesINT - Copy selected plots for documentation and visualization in wiki (custom rule) ####
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# Define the mapping of input to output files
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CorcesINT_plots_map = {
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"filtered.png": "results/CorcesINT/spilterlize_integrate/all/plots/filtered.png",
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"normupperquartile_integrated.png": "results/CorcesINT/spilterlize_integrate/all/plots/normupperquartile_integrated.png",
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"filtered_CFA.png": "results/CorcesINT/spilterlize_integrate/all/plots/filtered_CFA.png",
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"normupperquartile_integrated_CFA.png": "results/CorcesINT/spilterlize_integrate/all/plots/normupperquartile_integrated_CFA.png",
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"normupperquartile_integrated_PCA_cell_type.png": "results/CorcesINT/unsupervised_analysis/normupperquartile_integrated/PCA/plots/PCA_auto_0.9_2/metadata/cell_type.png",
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"normupperquartile_integrated_UMAP_cell_type.png": "results/CorcesINT/unsupervised_analysis/normupperquartile_integrated/UMAP/plots/UMAP_correlation_15_0.1_2/metadata/cell_type.png",
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"normupperquartile_integrated_PCA_modality.png": "results/CorcesINT/unsupervised_analysis/normupperquartile_integrated/PCA/plots/PCA_auto_0.9_2/metadata/modality.png",
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"normupperquartile_integrated_UMAP_modality.png": "results/CorcesINT/unsupervised_analysis/normupperquartile_integrated/UMAP/plots/UMAP_correlation_15_0.1_2/metadata/modality.png",
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"dea_stats.png": "results/CorcesINT/dea_limma/normupperquartile_integrated/plots/stats.png",
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"markerGenes.png": "results/CorcesINT/dea_limma/normupperquartile_integrated/plots/heatmap/markerGenes.png",
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"HSC_correlation.png": "results/CorcesINT/special_analysis/correlation_plots/HSC_correlation.png",
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"Mono_correlation.png": "results/CorcesINT/special_analysis/correlation_plots/Mono_correlation.png",
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"cell_types_GO_Biological_Process_2025_summary.png": "results/CorcesINT/enrichment_analysis/cell_types/preranked_GSEApy/GO_Biological_Process_2025/cell_types_GO_Biological_Process_2025_summary.png",
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"cell_types_ReactomePathways_summary.png": "results/CorcesINT/enrichment_analysis/cell_types/preranked_GSEApy/ReactomePathways/cell_types_ReactomePathways_summary.png",
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"Mono_EP.png": "results/CorcesINT/enrichment_analysis/Mono_EP/RcisTarget/hg38_500bp_up_100bp_down_v10clust/Mono_EP_hg38_500bp_up_100bp_down_v10clust.png",
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"Mono_TA.png": "results/CorcesINT/enrichment_analysis/Mono_TA/RcisTarget/hg38_500bp_up_100bp_down_v10clust/Mono_TA_hg38_500bp_up_100bp_down_v10clust.png",
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}
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# Copy input to outputs to include the plots in the repo and wiki
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# This rule can only be used for docs after all results (including untracked ones: volcano and unsuervised analysis plots)
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# have been generated (i.e. leave commented in the Snakefile's target rule until the end/last iteration)
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rule CorcesINT_plots:
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input:
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[CorcesINT_plots_map[plot] for plot in CorcesINT_plots_map]
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output:
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[f"docs/CorcesINT/{plot}" for plot in CorcesINT_plots_map]
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resources:
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mem_mb="1000",
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threads: config.get("threads", 1)
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log:
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"logs/rules/CorcesINT_plots.log",
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run:
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for i, o in zip(input, output):
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shell(f"cp {i} {o}")

‎workflow/rules/CorcesRNA.smk‎

Lines changed: 0 additions & 40 deletions
Original file line numberDiff line numberDiff line change
@@ -90,43 +90,3 @@ rule CorcesRNA_reconstruct_lineage:
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os.path.join("logs","rules","CorcesRNA_reconstruct_lineage.log"),
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script:
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"../scripts/crossprediction.py"
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#### CorcesRNA - Copy selected plots for documentation and visualization in wiki (custom rule) ####
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# Define the mapping of input to output files
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CorcesRNA_plots_map = {
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"sample_annotation.png": "results/CorcesRNA/rnaseq_pipeline/report/sample_annotation.png",
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"CD34.svg": "results/CorcesRNA/genome_tracks/tracks/CD34.svg",
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"MS4A1.svg": "results/CorcesRNA/genome_tracks/tracks/MS4A1.svg",
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"filtered.png": "results/CorcesRNA/spilterlize_integrate/all/plots/filtered.png",
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"normCQN_integrated.png": "results/CorcesRNA/spilterlize_integrate/all/plots/normCQN_integrated.png",
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"filtered_CFA.png": "results/CorcesRNA/spilterlize_integrate/all/plots/filtered_CFA.png",
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"normCQN_integrated_CFA.png": "results/CorcesRNA/spilterlize_integrate/all/plots/normCQN_integrated_CFA.png",
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"normCQN_integrated_PCA.png": "results/CorcesRNA/unsupervised_analysis/normCQN_integrated/PCA/plots/PCA_auto_0.9_2/metadata/cell_type.png",
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"normCQN_integrated_HVF_PCA.png": "results/CorcesRNA/unsupervised_analysis/normCQN_integrated_HVF/PCA/plots/PCA_auto_0.9_2/metadata/cell_type.png",
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"normCQN_integrated_UMAP.png": "results/CorcesRNA/unsupervised_analysis/normCQN_integrated/UMAP/plots/UMAP_correlation_15_0.1_2/metadata/cell_type.png",
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"normCQN_integrated_HVF_UMAP.png": "results/CorcesRNA/unsupervised_analysis/normCQN_integrated_HVF/UMAP/plots/UMAP_correlation_15_0.1_2/metadata/cell_type.png",
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"dea_stats.png": "results/CorcesRNA/dea_limma/normCQN_OvA_cell_type/plots/stats.png",
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"markerGenes.png": "results/CorcesRNA/dea_limma/normCQN_OvA_cell_type/plots/heatmap/markerGenes.png",
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"Bcell_ReactomePathways.png": "results/CorcesRNA/enrichment_analysis/Bcell/preranked_GSEApy/ReactomePathways/Bcell_ReactomePathways.png",
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"Bcell_Azimuth_2023.png": "results/CorcesRNA/enrichment_analysis/Bcell/preranked_GSEApy/Azimuth_2023/Bcell_Azimuth_2023.png",
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"cell_types_Azimuth_2023_summary.png": "results/CorcesRNA/enrichment_analysis/cell_types/preranked_GSEApy/Azimuth_2023/cell_types_Azimuth_2023_summary.png",
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"cell_types_ReactomePathways_summary.png": "results/CorcesRNA/enrichment_analysis/cell_types/preranked_GSEApy/ReactomePathways/cell_types_ReactomePathways_summary.png",
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"crossprediction_graph.png": "results/CorcesRNA/special_analyses/crossprediction/graph.png",
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}
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# Copy input to outputs to include the plots in the repo and wiki
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# This rule can only be used for docs after all results (including untracked ones: volcano and unsupervised analysis plots)
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# have been generated (i.e. leave commented in the Snakefile's target rule until the end/last iteration)
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rule CorcesRNA_plots:
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input:
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[CorcesRNA_plots_map[plot] for plot in CorcesRNA_plots_map]
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output:
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[f"docs/CorcesRNA/{plot}" for plot in CorcesRNA_plots_map]
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resources:
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mem_mb="1000",
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threads: config.get("threads", 1)
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log:
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"logs/rules/CorcesRNA_plots.log",
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run:
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for i, o in zip(input, output):
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shell(f"cp {i} {o}")

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