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Snakefile
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wildcard_constraints:
subset='all|erpos_her2neg|fibrosis'
rule all:
input:
'plots/boxplot_stroma_all_density_clinical_variables.pdf',
'plots/boxplot_dcis_all_density_clinical_variables.pdf',
'plots/boxplot_stroma_fibrosis_density_clinical_variables.pdf',
'plots/boxplot_dcis_fibrosis_density_clinical_variables.pdf',
'plots/boxplot_stroma_erpos_her2neg_density_clinical_variables.pdf',
'plots/boxplot_dcis_erpos_her2neg_density_clinical_variables.pdf',
'results/significance_stroma_ratio_all.xlsx',
'results/significance_dcis_ratio_all.xlsx',
'plots/heatmap_density_Stroma.pdf',
'plots/heatmap_density_DCIS.pdf',
'results/significance_til_density_all.xlsx',
'results/significance_stroma_densgrade_all.xlsx',
rule boxplot_dens_clin_stroma:
output:
plot='plots/boxplot_stroma_{subset}_density_clinical_variables.pdf',
tests='results/significance_stroma_{subset}.xlsx',
stats='results/summary_stats_stroma_{subset}.xlsx',
input:
density='data/cell_density_Stroma.tsv',
clinical='data/clin_DBL_v_str_dens.tsv',
script='src/beeswarm_clin_dens.R',
shell:
'Rscript {input.script} {input.density} Tissue {input.clinical}'
' {wildcards.subset} {output.plot} {output.stats} {output.tests}'
rule boxplot_dens_clin_dcis:
output:
plot='plots/boxplot_dcis_{subset}_density_clinical_variables.pdf',
tests='results/significance_dcis_{subset}.xlsx',
stats='results/summary_stats_dcis_{subset}.xlsx',
input:
density='data/cell_density_DCIS.tsv',
clinical='data/clin_DBL_v_str_dens.tsv',
script='src/beeswarm_clin_dens.R',
shell:
'Rscript {input.script} {input.density} DCIS {input.clinical}'
' {wildcards.subset} {output.plot} {output.stats} {output.tests}'
rule ratios_clin_stroma:
output:
tests='results/significance_stroma_ratio_{subset}.xlsx',
stats='results/summary_stats_stroma_ratio_{subset}.xlsx',
input:
density='data/cell_density_Stroma.tsv',
clinical='data/clin_DBL_v_str_dens.tsv',
script='src/ratios.R',
shell:
'Rscript {input.script} {input.density} Tissue {input.clinical}'
' {wildcards.subset} {output.stats} {output.tests}'
rule ratios_clin_dcis:
output:
tests='results/significance_dcis_ratio_{subset}.xlsx',
stats='results/summary_stats_dcis_ratio_{subset}.xlsx',
input:
density='data/cell_density_DCIS.tsv',
clinical='data/clin_DBL_v_str_dens.tsv',
script='src/ratios.R',
shell:
'Rscript {input.script} {input.density} DCIS {input.clinical}'
' {wildcards.subset} {output.stats} {output.tests}'
rule dens_grade_test:
output:
tests='results/significance_stroma_densgrade_{subset}.xlsx',
input:
density='data/cell_density_Stroma.tsv',
clinical='data/clin_DBL_v_str_dens.tsv',
script='src/dens_and_grade.R',
shell:
'Rscript {input.script} {input.density} Tissue {input.clinical}'
' {wildcards.subset} {output.tests}'
rule pathologist_scored_tils:
output:
tests='results/significance_til_density_{subset}.xlsx',
input:
density='data/cell_density_Stroma.tsv',
clinical='data/clin_DBL_v_str_dens.tsv',
til_scores='data/20220324_TILscores_revised.tsv',
script='src/til_stats.R',
shell:
'Rscript {input.script} {input.density} Tissue {input.clinical}'
' {wildcards.subset} {input.til_scores} {output.tests}'
rule clustering:
output:
'plots/heatmap_density_Stroma.pdf',
'plots/heatmap_density_DCIS.pdf',
input:
density_stroma='data/cell_density_Stroma.tsv',
density_dcis='data/cell_density_DCIS.tsv',
clinical='data/clin_DBL_v_str_dens.tsv',
script='src/clustering.R',
shell:
'Rscript {input.script}'