SHELL:=/bin/bash
.PHONY: all input_files

all: combined_plots/combined_summary_adduct_ion_composition.pdf \
combined_plots_pureDHB_subtraction/combined_pureDHB_subtraction_summary_adduct_ion_composition.pdf \
combined_plots/combined_summary_adduct_ion_composition_correlation_cutoff.pdf \
combined_plots_pureDHB_subtraction/combined_pureDHB_subtraction_summary_adduct_ion_composition_correlation_cutoff.pdf \
combined_plots_by_type combined_plots_by_type_pureDHB_subtraction

## Combine plots ---------------------------------------------------------------

# Adduct ion composition as a fraction of total peaks per dataset - by correlation value
combined_plots/combined_summary_adduct_ion_composition_correlation_cutoff.pdf \
combined_plots/combined_summary_adduct_ion_composition_correlation_cutoff.tsv: combined_plots
	Rscript scripts/do_summary_adduct_ion_plot_by_correlation.R \
	combined_plots/combined_ \
	plots/01_Mussel_DHB1_adduct_matches_by_correlation.tsv \
	plots/02_Mussel_DHB2_adduct_matches_by_correlation.tsv \
	plots/03_Mussel_DHB3_adduct_matches_by_correlation.tsv \
	plots/04_Mussel_DHB4_adduct_matches_by_correlation.tsv \
	plots/05_Mussel_CHCA1_adduct_matches_by_correlation.tsv \
	plots/06_Mussel_CHCA2_adduct_matches_by_correlation.tsv \
	plots/07_Mussel_CHCA3_adduct_matches_by_correlation.tsv \
	plots/08_Mussel_CHCA4_adduct_matches_by_correlation.tsv \
	plots/09_Brain_Bruker_DHB_adduct_matches_by_correlation.tsv \
	plots/10_Brain_Thermo_DHB_adduct_matches_by_correlation.tsv \
	plots/11_Brain_MALDI_Waters_DHB_adduct_matches_by_correlation.tsv \
	plots/12_Brain_MALDI2_Waters_DHB_adduct_matches_by_correlation.tsv \
	plots/13_Testis_DHB_adduct_matches_by_correlation.tsv \
	plots/14_Cocoa_DHB_adduct_matches_by_correlation.tsv \
	plots/15_Seagrass_DHB_adduct_matches_by_correlation.tsv \
	plots/16_Fungus_DHB_adduct_matches_by_correlation.tsv \
	plots/17_MetaMix_DHB_adduct_matches_by_correlation.tsv \
	plots/18_MetaMix_CHCA_adduct_matches_by_correlation.tsv

# Adduct ion composition when pure DHB compounds are subtracted from the peaklist - by correlation value
combined_plots_pureDHB_subtraction/combined_pureDHB_subtraction_summary_adduct_ion_composition_correlation_cutoff.pdf \
combined_plots_pureDHB_subtraction/combined_pureDHB_subtraction_summary_adduct_ion_composition_correlation_cutoff.tsv: combined_plots_pureDHB_subtraction
	Rscript scripts/do_summary_adduct_ion_plot_by_correlation.R \
	combined_plots_pureDHB_subtraction/combined_pureDHB_subtraction_ \
	plots_pureDHB_subtraction/01_Mussel_DHB1_adduct_matches_by_correlation.tsv \
	plots_pureDHB_subtraction/02_Mussel_DHB2_adduct_matches_by_correlation.tsv \
	plots_pureDHB_subtraction/03_Mussel_DHB3_adduct_matches_by_correlation.tsv \
	plots_pureDHB_subtraction/04_Mussel_DHB4_adduct_matches_by_correlation.tsv \
	plots_pureDHB_subtraction/05_Mussel_CHCA1_adduct_matches_by_correlation.tsv \
	plots_pureDHB_subtraction/06_Mussel_CHCA2_adduct_matches_by_correlation.tsv \
	plots_pureDHB_subtraction/07_Mussel_CHCA3_adduct_matches_by_correlation.tsv \
	plots_pureDHB_subtraction/08_Mussel_CHCA4_adduct_matches_by_correlation.tsv \
	plots_pureDHB_subtraction/09_Brain_Bruker_DHB_adduct_matches_by_correlation.tsv \
	plots_pureDHB_subtraction/10_Brain_Thermo_DHB_adduct_matches_by_correlation.tsv \
	plots_pureDHB_subtraction/11_Brain_MALDI_Waters_DHB_adduct_matches_by_correlation.tsv \
	plots_pureDHB_subtraction/12_Brain_MALDI2_Waters_DHB_adduct_matches_by_correlation.tsv \
	plots_pureDHB_subtraction/13_Testis_DHB_adduct_matches_by_correlation.tsv \
	plots_pureDHB_subtraction/14_Cocoa_DHB_adduct_matches_by_correlation.tsv \
	plots_pureDHB_subtraction/15_Seagrass_DHB_adduct_matches_by_correlation.tsv \
	plots_pureDHB_subtraction/16_Fungus_DHB_adduct_matches_by_correlation.tsv \
	plots_pureDHB_subtraction/17_MetaMix_DHB_adduct_matches_by_correlation.tsv \
	plots_pureDHB_subtraction/18_MetaMix_CHCA_adduct_matches_by_correlation.tsv

# Adduct ion composition as a fraction of total peaks per dataset
combined_plots/combined_summary_adduct_ion_composition.pdf \
combined_plots/combined_summary_adduct_ion_composition.tsv: combined_plots
	Rscript scripts/do_summary_adduct_ion_plot.R \
	combined_plots/combined_ \
	plots/01_Mussel_DHB1_adduct_matches_by_qvalue.tsv \
	plots/02_Mussel_DHB2_adduct_matches_by_qvalue.tsv \
	plots/03_Mussel_DHB3_adduct_matches_by_qvalue.tsv \
	plots/04_Mussel_DHB4_adduct_matches_by_qvalue.tsv \
	plots/05_Mussel_CHCA1_adduct_matches_by_qvalue.tsv \
	plots/06_Mussel_CHCA2_adduct_matches_by_qvalue.tsv \
	plots/07_Mussel_CHCA3_adduct_matches_by_qvalue.tsv \
	plots/08_Mussel_CHCA4_adduct_matches_by_qvalue.tsv \
	plots/09_Brain_Bruker_DHB_adduct_matches_by_qvalue.tsv \
	plots/10_Brain_Thermo_DHB_adduct_matches_by_qvalue.tsv \
	plots/11_Brain_MALDI_Waters_DHB_adduct_matches_by_qvalue.tsv \
	plots/12_Brain_MALDI2_Waters_DHB_adduct_matches_by_qvalue.tsv \
	plots/13_Testis_DHB_adduct_matches_by_qvalue.tsv \
	plots/14_Cocoa_DHB_adduct_matches_by_qvalue.tsv \
	plots/15_Seagrass_DHB_adduct_matches_by_qvalue.tsv \
	plots/16_Fungus_DHB_adduct_matches_by_qvalue.tsv \
	plots/17_MetaMix_DHB_adduct_matches_by_qvalue.tsv \
	plots/18_MetaMix_CHCA_adduct_matches_by_qvalue.tsv

# Adduct ion composition when pure DHB compounds are subtracted from the peaklist
combined_plots_pureDHB_subtraction/combined_pureDHB_subtraction_summary_adduct_ion_composition.pdf \
combined_plots_pureDHB_subtraction/combined_pureDHB_subtraction_summary_adduct_ion_composition.tsv: combined_plots_pureDHB_subtraction
	Rscript scripts/do_summary_adduct_ion_plot.R \
	combined_plots_pureDHB_subtraction/combined_pureDHB_subtraction_ \
	plots_pureDHB_subtraction/01_Mussel_DHB1_adduct_matches_by_qvalue.tsv \
	plots_pureDHB_subtraction/02_Mussel_DHB2_adduct_matches_by_qvalue.tsv \
	plots_pureDHB_subtraction/03_Mussel_DHB3_adduct_matches_by_qvalue.tsv \
	plots_pureDHB_subtraction/04_Mussel_DHB4_adduct_matches_by_qvalue.tsv \
	plots_pureDHB_subtraction/05_Mussel_CHCA1_adduct_matches_by_qvalue.tsv \
	plots_pureDHB_subtraction/06_Mussel_CHCA2_adduct_matches_by_qvalue.tsv \
	plots_pureDHB_subtraction/07_Mussel_CHCA3_adduct_matches_by_qvalue.tsv \
	plots_pureDHB_subtraction/08_Mussel_CHCA4_adduct_matches_by_qvalue.tsv \
	plots_pureDHB_subtraction/09_Brain_Bruker_DHB_adduct_matches_by_qvalue.tsv \
	plots_pureDHB_subtraction/10_Brain_Thermo_DHB_adduct_matches_by_qvalue.tsv \
	plots_pureDHB_subtraction/11_Brain_MALDI_Waters_DHB_adduct_matches_by_qvalue.tsv \
	plots_pureDHB_subtraction/12_Brain_MALDI2_Waters_DHB_adduct_matches_by_qvalue.tsv \
	plots_pureDHB_subtraction/13_Testis_DHB_adduct_matches_by_qvalue.tsv \
	plots_pureDHB_subtraction/14_Cocoa_DHB_adduct_matches_by_qvalue.tsv \
	plots_pureDHB_subtraction/15_Seagrass_DHB_adduct_matches_by_qvalue.tsv \
	plots_pureDHB_subtraction/16_Fungus_DHB_adduct_matches_by_qvalue.tsv \
	plots_pureDHB_subtraction/17_MetaMix_DHB_adduct_matches_by_qvalue.tsv \
	plots_pureDHB_subtraction/18_MetaMix_CHCA_adduct_matches_by_qvalue.tsv

combined_plots_by_type_pureDHB_subtraction = combined_plots_pureDHB_subtraction/combined_adduct_corr_control.pdf \
combined_plots_pureDHB_subtraction/combined_adducts_diffs_qvalue_cutoffs.pdf \
combined_plots_pureDHB_subtraction/combined_adducts_diffs_correlation_cutoffs.pdf \
combined_plots_pureDHB_subtraction/combined_adducts_ions_qvalue_cutoffs.pdf \
combined_plots_pureDHB_subtraction/combined_adducts_ions_correlation_cutoffs.pdf \
combined_plots_pureDHB_subtraction/combined_massdiff_histogram.pdf \
combined_plots_pureDHB_subtraction/combined_massdiff_histogram_0_200.pdf \
combined_plots_pureDHB_subtraction/combined_mass_spectrum.pdf \
combined_plots_pureDHB_subtraction/combined_mass_spectrum_0_1200_postfilter.pdf \
combined_plots_pureDHB_subtraction/combined_mass_spectrum_DHB_adducts_correlation_cutoff.pdf \
combined_plots_pureDHB_subtraction/combined_mass_spectrum_DHB_adducts_qvalue_cutoff.pdf \
combined_plots_pureDHB_subtraction/combined_pvalue_histogram.pdf \
combined_plots_pureDHB_subtraction/combined_weightedHistogram.pdf \
combined_plots_pureDHB_subtraction/combined_weightedHistogram_0_200.pdf

combined_plots_pureDHB_subtraction/combined_adduct_corr_control.pdf : $(combined_plots_pureDHB_subtraction)
	pdftk plots_pureDHB_subtraction/*_adduct_corr_control.pdf cat output $@
combined_plots_pureDHB_subtraction/combined_adducts_diffs_qvalue_cutoffs.pdf : $(combined_plots_pureDHB_subtraction)
	pdftk plots_pureDHB_subtraction/*_adducts_diffs_qvalue_cutoffs.pdf cat output $@
combined_plots_pureDHB_subtraction/combined_adducts_diffs_correlation_cutoffs.pdf : $(combined_plots_pureDHB_subtraction)
	pdftk plots_pureDHB_subtraction/*_adducts_diffs_correlation_cutoffs.pdf cat output $@
combined_plots_pureDHB_subtraction/combined_adducts_ions_qvalue_cutoffs.pdf : $(combined_plots_pureDHB_subtraction)
	pdftk plots_pureDHB_subtraction/*_adducts_ions_qvalue_cutoffs.pdf cat output $@
combined_plots_pureDHB_subtraction/combined_adducts_ions_correlation_cutoffs.pdf : $(combined_plots_pureDHB_subtraction)
	pdftk plots_pureDHB_subtraction/*_adducts_ions_correlation_cutoffs.pdf cat output $@
combined_plots_pureDHB_subtraction/combined_massdiff_histogram.pdf : $(combined_plots_pureDHB_subtraction)
	pdftk plots_pureDHB_subtraction/*_massdiff_histogram.pdf cat output $@
combined_plots_pureDHB_subtraction/combined_massdiff_histogram_0_200.pdf : $(combined_plots_pureDHB_subtraction)
	pdftk plots_pureDHB_subtraction/*_massdiff_histogram_0_200.pdf cat output $@
combined_plots_pureDHB_subtraction/combined_mass_spectrum.pdf : $(combined_plots_pureDHB_subtraction)
	pdftk plots_pureDHB_subtraction/*_mass_spectrum.pdf cat output $@
combined_plots_pureDHB_subtraction/combined_mass_spectrum_0_1200_postfilter.pdf : $(combined_plots_pureDHB_subtraction)
	pdftk plots_pureDHB_subtraction/*_mass_spectrum_0_1200_postfilter.pdf cat output $@
combined_plots_pureDHB_subtraction/combined_mass_spectrum_DHB_adducts_correlation_cutoff.pdf : $(combined_plots_pureDHB_subtraction)
	pdftk plots_pureDHB_subtraction/*_mass_spectrum_DHB_adducts_correlation_cutoff.pdf cat output $@
combined_plots_pureDHB_subtraction/combined_mass_spectrum_DHB_adducts_qvalue_cutoff.pdf : $(combined_plots_pureDHB_subtraction)
	pdftk plots_pureDHB_subtraction/*_mass_spectrum_DHB_adducts_qvalue_cutoff.pdf cat output $@
combined_plots_pureDHB_subtraction/combined_pvalue_histogram.pdf : $(combined_plots_pureDHB_subtraction)
	pdftk plots_pureDHB_subtraction/*_pvalue_histogram.pdf cat output $@
combined_plots_pureDHB_subtraction/combined_weightedHistogram.pdf : $(weighted_histograms_pureDHB_subtraction)
	pdftk plots_pureDHB_subtraction/*_weightedHistogram.pdf cat output $@
combined_plots_pureDHB_subtraction/combined_weightedHistogram_0_200.pdf : $(weighted_histograms_pureDHB_subtraction)
	pdftk plots_pureDHB_subtraction/*_weightedHistogram_0_200.pdf cat output $@

combined_plots_by_type = combined_plots/combined_adduct_corr_control.pdf \
combined_plots/combined_adducts_diffs_qvalue_cutoffs.pdf \
combined_plots/combined_adducts_diffs_correlation_cutoffs.pdf \
combined_plots/combined_adducts_ions_qvalue_cutoffs.pdf \
combined_plots/combined_adducts_ions_correlation_cutoffs.pdf \
combined_plots/combined_massdiff_histogram.pdf \
combined_plots/combined_massdiff_histogram_0_200.pdf \
combined_plots/combined_mass_spectrum.pdf \
combined_plots/combined_mass_spectrum_0_1200.pdf \
combined_plots/combined_mass_spectrum_DHB_adducts_correlation_cutoff.pdf \
combined_plots/combined_mass_spectrum_DHB_adducts_qvalue_cutoff.pdf \
combined_plots/combined_pvalue_histogram.pdf \
combined_plots/combined_weightedHistogram.pdf \
combined_plots/combined_weightedHistogram_0_200.pdf

combined_plots/combined_adduct_corr_control.pdf: $(combined_plots)
	pdftk plots/*_adduct_corr_control.pdf cat output $@
combined_plots/combined_adducts_diffs_qvalue_cutoffs.pdf: $(combined_plots)
	pdftk plots/*_adducts_diffs_qvalue_cutoffs.pdf cat output $@
combined_plots/combined_adducts_diffs_correlation_cutoffs.pdf: $(combined_plots)
	pdftk plots/*_adducts_diffs_correlation_cutoffs.pdf cat output $@
combined_plots/combined_adducts_ions_qvalue_cutoffs.pdf: $(combined_plots)
	pdftk plots/*_adducts_ions_qvalue_cutoffs.pdf cat output $@
combined_plots/combined_adducts_ions_correlation_cutoffs.pdf: $(combined_plots)
	pdftk plots/*_adducts_ions_correlation_cutoffs.pdf cat output $@
combined_plots/combined_massdiff_histogram.pdf: $(combined_plots)
	pdftk plots/*_massdiff_histogram.pdf cat output $@
combined_plots/combined_massdiff_histogram_0_200.pdf: $(combined_plots)
	pdftk plots/*_massdiff_histogram_0_200.pdf cat output $@
combined_plots/combined_mass_spectrum.pdf: $(combined_plots)
	pdftk plots/*_mass_spectrum.pdf cat output $@
combined_plots/combined_mass_spectrum_0_1200.pdf: $(combined_plots)
	pdftk plots/*_mass_spectrum_0_1200.pdf cat output $@
combined_plots/combined_mass_spectrum_DHB_adducts_correlation_cutoff.pdf: $(combined_plots)
	pdftk plots/*_mass_spectrum_DHB_adducts_correlation_cutoff.pdf cat output $@
combined_plots/combined_mass_spectrum_DHB_adducts_qvalue_cutoff.pdf: $(combined_plots)
	pdftk plots/*_mass_spectrum_DHB_adducts_qvalue_cutoff.pdf cat output $@
combined_plots/combined_pvalue_histogram.pdf: $(combined_plots)
	pdftk plots/*_pvalue_histogram.pdf cat output $@
combined_plots/combined_weightedHistogram.pdf: $(weighted_histograms)
	pdftk plots/*_weightedHistogram.pdf cat output $@
combined_plots/combined_weightedHistogram_0_200.pdf: $(weighted_histograms)
	pdftk plots/*_weightedHistogram_0_200.pdf cat output $@

combined_plots = combined_plots/01_Mussel_DHB1_combined_plots.pdf \
plots/02_Mussel_DHB2_combined_plots.pdf \
plots/03_Mussel_DHB3_combined_plots.pdf \
plots/04_Mussel_DHB4_combined_plots.pdf \
plots/05_Mussel_CHCA1_combined_plots.pdf \
plots/06_Mussel_CHCA2_combined_plots.pdf \
plots/07_Mussel_CHCA3_combined_plots.pdf \
plots/08_Mussel_CHCA4_combined_plots.pdf \
plots/09_Brain_Bruker_DHB_combined_plots.pdf \
plots/10_Brain_Thermo_DHB_weightedHistogram.pdf \
plots/11_Brain_MALDI_Waters_DHB_combined_plots.pdf \
plots/12_Brain_MALDI2_Waters_DHB_weightedHistogram.pdf \
plots/13_Testis_DHB_weightedHistogram.pdf \
plots/14_Cocoa_DHB_weightedHistogram.pdf \
plots/15_Seagrass_DHB_weightedHistogram.pdf \
plots/16_Fungus_DHB_weightedHistogram.pdf \
plots/17_MetaMix_DHB_weightedHistogram.pdf \
plots/18_MetaMix_CHCA_weightedHistogram.pdf

combined_plots_pureDHB_subtraction = combined_plots_pureDHB_subtraction/01_Mussel_DHB1_combined_plots.pdf \
plots_pureDHB_subtraction/02_Mussel_DHB2_combined_plots.pdf \
plots_pureDHB_subtraction/03_Mussel_DHB3_combined_plots.pdf \
plots_pureDHB_subtraction/04_Mussel_DHB4_combined_plots.pdf \
plots_pureDHB_subtraction/05_Mussel_CHCA1_combined_plots.pdf \
plots_pureDHB_subtraction/06_Mussel_CHCA2_combined_plots.pdf \
plots_pureDHB_subtraction/07_Mussel_CHCA3_combined_plots.pdf \
plots_pureDHB_subtraction/08_Mussel_CHCA4_combined_plots.pdf \
plots_pureDHB_subtraction/09_Brain_Bruker_DHB_combined_plots.pdf \
plots_pureDHB_subtraction/10_Brain_Thermo_DHB_weightedHistogram.pdf \
plots_pureDHB_subtraction/11_Brain_MALDI_Waters_DHB_combined_plots.pdf \
plots_pureDHB_subtraction/12_Brain_MALDI2_Waters_DHB_weightedHistogram.pdf \
plots_pureDHB_subtraction/13_Testis_DHB_weightedHistogram.pdf \
plots_pureDHB_subtraction/14_Cocoa_DHB_weightedHistogram.pdf \
plots_pureDHB_subtraction/15_Seagrass_DHB_weightedHistogram.pdf \
plots_pureDHB_subtraction/16_Fungus_DHB_weightedHistogram.pdf \
plots_pureDHB_subtraction/17_MetaMix_DHB_weightedHistogram.pdf \
plots_pureDHB_subtraction/18_MetaMix_CHCA_weightedHistogram.pdf

## Weighted histograms ---------------------------------------------------------

weighted_histograms = plots/01_Mussel_DHB1_weightedHistogram.pdf \
plots/02_Mussel_DHB2_weightedHistogram.pdf \
plots/03_Mussel_DHB3_weightedHistogram.pdf \
plots/04_Mussel_DHB4_weightedHistogram.pdf \
plots/05_Mussel_CHCA1_weightedHistogram.pdf \
plots/06_Mussel_CHCA2_weightedHistogram.pdf \
plots/07_Mussel_CHCA3_weightedHistogram.pdf \
plots/08_Mussel_CHCA4_weightedHistogram.pdf \
plots/09_Brain_Bruker_DHB_weightedHistogram.pdf \
plots/10_Brain_Thermo_DHB_weightedHistogram.pdf \
plots/11_Brain_MALDI_Waters_DHB_weightedHistogram.pdf \
plots/12_Brain_MALDI2_Waters_DHB_weightedHistogram.pdf \
plots/13_Testis_DHB_weightedHistogram.pdf \
plots/14_Cocoa_DHB_weightedHistogram.pdf \
plots/15_Seagrass_DHB_weightedHistogram.pdf \
plots/16_Fungus_DHB_weightedHistogram.pdf \
plots/17_MetaMix_DHB_weightedHistogram.pdf \
plots/18_MetaMix_CHCA_weightedHistogram.pdf 

plots/%.filter_weightedHistogram.pdf: corrtest_Rdata/%.filter.Rworkspace.Rda
	cd $(@D); Rscript ../scripts/do_weighted_histogram.R ../$<

weighted_histograms_pureDHB_subtraction = plots_pureDHB_subtraction/01_Mussel_DHB1_pureDHB_subtraction_weightedHistogram.pdf \
plots_pureDHB_subtraction/02_Mussel_DHB2_pureDHB_subtraction_weightedHistogram.pdf \
plots_pureDHB_subtraction/03_Mussel_DHB3_pureDHB_subtraction_weightedHistogram.pdf \
plots_pureDHB_subtraction/04_Mussel_DHB4_pureDHB_subtraction_weightedHistogram.pdf \
plots_pureDHB_subtraction/05_Mussel_CHCA1_pureDHB_subtraction_weightedHistogram.pdf \
plots_pureDHB_subtraction/06_Mussel_CHCA2_pureDHB_subtraction_weightedHistogram.pdf \
plots_pureDHB_subtraction/07_Mussel_CHCA3_pureDHB_subtraction_weightedHistogram.pdf \
plots_pureDHB_subtraction/08_Mussel_CHCA4_pureDHB_subtraction_weightedHistogram.pdf \
plots_pureDHB_subtraction/09_Brain_Bruker_DHB_pureDHB_subtraction_weightedHistogram.pdf \
plots_pureDHB_subtraction/10_Brain_Thermo_DHB_pureDHB_subtraction_weightedHistogram.pdf \
plots_pureDHB_subtraction/11_Brain_MALDI_Waters_DHB_pureDHB_subtraction_weightedHistogram.pdf \
plots_pureDHB_subtraction/12_Brain_MALDI2_Waters_DHB_pureDHB_subtraction_weightedHistogram.pdf \
plots_pureDHB_subtraction/13_Testis_DHB_pureDHB_subtraction_weightedHistogram.pdf \
plots_pureDHB_subtraction/14_Cocoa_DHB_pureDHB_subtraction_weightedHistogram.pdf \
plots_pureDHB_subtraction/15_Seagrass_DHB_pureDHB_subtraction_weightedHistogram.pdf \
plots_pureDHB_subtraction/16_Fungus_DHB_pureDHB_subtraction_weightedHistogram.pdf \
plots_pureDHB_subtraction/17_MetaMix_DHB_pureDHB_subtraction_weightedHistogram.pdf \
plots_pureDHB_subtraction/18_MetaMix_CHCA_pureDHB_subtraction_weightedHistogram.pdf 

plots_pureDHB_subtraction/01_Mussel_DHB1_pureDHB_subtraction_weightedHistogram.pdf: corrtest_Rdata/corrtest_Rdata/01_Mussel_DHB1_ppm.filter.Rworkspace.Rda $(pure_DHB_dataset)
	cd $(@D); Rscript ../scripts/do_weighted_histogram_pureDHB_subtraction.R 2.777 ../$<
plots_pureDHB_subtraction/02_Mussel_DHB2_pureDHB_subtraction_weightedHistogram.pdf: corrtest_Rdata/02_Mussel_DHB2_ppm.filter.Rworkspace.Rda $(pure_DHB_dataset)
	cd $(@D); Rscript ../scripts/do_weighted_histogram_pureDHB_subtraction.R 4.115 ../$<
plots_pureDHB_subtraction/03_Mussel_DHB3_pureDHB_subtraction_weightedHistogram.pdf: corrtest_Rdata/03_Mussel_DHB3_ppm.filter.Rworkspace.Rda $(pure_DHB_dataset)
	cd $(@D); Rscript ../scripts/do_weighted_histogram_pureDHB_subtraction.R 9.410 ../$<
plots_pureDHB_subtraction/04_Mussel_DHB4_pureDHB_subtraction_weightedHistogram.pdf: corrtest_Rdata/04_Mussel_DHB4_no.filter.Rworkspace.Rda $(pure_DHB_dataset)
	cd $(@D); Rscript ../scripts/do_weighted_histogram_pureDHB_subtraction.R 1 ../$<
plots_pureDHB_subtraction/05_Mussel_CHCA1_pureDHB_subtraction_weightedHistogram.pdf: corrtest_Rdata/05_Mussel_CHCA1_ppm.filter.Rworkspace.Rda $(pure_DHB_dataset)
	cd $(@D); Rscript ../scripts/do_weighted_histogram_pureDHB_subtraction.R 2 ../$<
plots_pureDHB_subtraction/06_Mussel_CHCA2_pureDHB_subtraction_weightedHistogram.pdf: corrtest_Rdata/06_Mussel_CHCA2_ppm.filter.Rworkspace.Rda $(pure_DHB_dataset)
	cd $(@D); Rscript ../scripts/do_weighted_histogram_pureDHB_subtraction.R 2.554 ../$<
plots_pureDHB_subtraction/07_Mussel_CHCA3_pureDHB_subtraction_weightedHistogram.pdf: corrtest_Rdata/07_Mussel_CHCA3_ppm.filter.Rworkspace.Rda $(pure_DHB_dataset)
	cd $(@D); Rscript ../scripts/do_weighted_histogram_pureDHB_subtraction.R 6.048 ../$<
plots_pureDHB_subtraction/08_Mussel_CHCA4_pureDHB_subtraction_weightedHistogram.pdf: corrtest_Rdata/08_Mussel_CHCA4_no.filter.Rworkspace.Rda $(pure_DHB_dataset)
	cd $(@D); Rscript ../scripts/do_weighted_histogram_pureDHB_subtraction.R 1 ../$<
plots_pureDHB_subtraction/09_Brain_Bruker_DHB_pureDHB_subtraction_weightedHistogram.pdf: corrtest_Rdata/09_Brain_Bruker_DHB_ppm.filter.Rworkspace.Rda $(pure_DHB_dataset)
	cd $(@D); Rscript ../scripts/do_weighted_histogram_pureDHB_subtraction.R 2.825 ../$<
plots_pureDHB_subtraction/10_Brain_Thermo_DHB_pureDHB_subtraction_weightedHistogram.pdf: corrtest_Rdata/10_Brain_Thermo_DHB_no.filter.Rworkspace.Rda $(pure_DHB_dataset)
	cd $(@D); Rscript ../scripts/do_weighted_histogram_pureDHB_subtraction.R 1 ../$<
plots_pureDHB_subtraction/11_Brain_MALDI_Waters_DHB_pureDHB_subtraction_weightedHistogram.pdf: corrtest_Rdata/11_Brain_MALDI_Waters_DHB_waters.filter.Rworkspace.Rda $(pure_DHB_dataset)
	cd $(@D); Rscript ../scripts/do_weighted_histogram_pureDHB_subtraction.R 5 ../$<
plots_pureDHB_subtraction/12_Brain_MALDI2_Waters_DHB_pureDHB_subtraction_weightedHistogram.pdf: corrtest_Rdata/12_Brain_MALDI2_Waters_DHB_waters.filter.Rworkspace.Rda $(pure_DHB_dataset)
	cd $(@D); Rscript ../scripts/do_weighted_histogram_pureDHB_subtraction.R 5 ../$<
plots_pureDHB_subtraction/13_Testis_DHB_pureDHB_subtraction_weightedHistogram.pdf: corrtest_Rdata/13_Testis_DHB_ppm.filter.Rworkspace.Rda $(pure_DHB_dataset)
	cd $(@D); Rscript ../scripts/do_weighted_histogram_pureDHB_subtraction.R 11.036 ../$<
plots_pureDHB_subtraction/14_Cocoa_DHB_pureDHB_subtraction_weightedHistogram.pdf: corrtest_Rdata/14_Cocoa_DHB_ppm.filter.Rworkspace.Rda $(pure_DHB_dataset)
	cd $(@D); Rscript ../scripts/do_weighted_histogram_pureDHB_subtraction.R 4.036 ../$<
plots_pureDHB_subtraction/15_Seagrass_DHB_pureDHB_subtraction_weightedHistogram.pdf: corrtest_Rdata/15_Seagrass_DHB_ppm.filter.Rworkspace.Rda $(pure_DHB_dataset)
	cd $(@D); Rscript ../scripts/do_weighted_histogram_pureDHB_subtraction.R 3.122 ../$<
plots_pureDHB_subtraction/16_Fungus_DHB_pureDHB_subtraction_weightedHistogram.pdf: corrtest_Rdata/16_Fungus_DHB_waters.filter.Rworkspace.Rda $(pure_DHB_dataset)
	cd $(@D); Rscript ../scripts/do_weighted_histogram_pureDHB_subtraction.R 5 ../$<
plots_pureDHB_subtraction/17_MetaMix_DHB_pureDHB_subtraction_weightedHistogram.pdf: corrtest_Rdata/17_MetaMix_DHB_no.filter.Rworkspace.Rda $(pure_DHB_dataset)
	cd $(@D); Rscript ../scripts/do_weighted_histogram_pureDHB_subtraction.R 1 ../$<
plots_pureDHB_subtraction/18_MetaMix_CHCA_pureDHB_subtraction_weightedHistogram.pdf: corrtest_Rdata/18_MetaMix_CHCA_no.filter.Rworkspace.Rda $(pure_DHB_dataset)
	cd $(@D); Rscript ../scripts/do_weighted_histogram_pureDHB_subtraction.R 1 ../$<

## Mass2adduct analysis and plots  ---------------------------------------------

plots/01_Mussel_DHB1_combined_plots.pdf: corrtest_Rdata/01_Mussel_DHB1_ppm.filter.Rworkspace.Rda $(pure_DHB_dataset)
	Rscript scripts/do_mass2adduct_analysis.R $< 2.777 355 plots/01_Mussel_DHB1
	pdftk plots/01_*.pdf cat output $@

plots/02_Mussel_DHB2_combined_plots.pdf: corrtest_Rdata/02_Mussel_DHB2_ppm.filter.Rworkspace.Rda $(pure_DHB_dataset)
	Rscript scripts/do_mass2adduct_analysis.R $< 4.115 500 plots/02_Mussel_DHB2
	pdftk plots/02_*.pdf cat output $@

plots/03_Mussel_DHB3_combined_plots.pdf: corrtest_Rdata/03_Mussel_DHB3_ppm.filter.Rworkspace.Rda $(pure_DHB_dataset)
	Rscript scripts/do_mass2adduct_analysis.R $< 9.410 315 plots/03_Mussel_DHB3
	pdftk plots/03_*.pdf cat output $@

plots/04_Mussel_DHB4_combined_plots.pdf: corrtest_Rdata/04_Mussel_DHB4_no.filter.Rworkspace.Rda $(pure_DHB_dataset)
	Rscript scripts/do_mass2adduct_analysis.R $< 1 150 plots/04_Mussel_DHB4
	pdftk plots/04_*.pdf cat output $@

plots/05_Mussel_CHCA1_combined_plots.pdf: corrtest_Rdata/05_Mussel_CHCA1_ppm.filter.Rworkspace.Rda $(pure_DHB_dataset)
	Rscript scripts/do_mass2adduct_analysis.R $< 2 355 plots/05_Mussel_CHCA1
	pdftk plots/05_*.pdf cat output $@

plots/06_Mussel_CHCA2_combined_plots.pdf: corrtest_Rdata/06_Mussel_CHCA2_ppm.filter.Rworkspace.Rda $(pure_DHB_dataset)
	Rscript scripts/do_mass2adduct_analysis.R $< 2.554 100 plots/06_Mussel_CHCA2
	pdftk plots/06_*.pdf cat output $@

plots/07_Mussel_CHCA3_combined_plots.pdf: corrtest_Rdata/07_Mussel_CHCA3_ppm.filter.Rworkspace.Rda $(pure_DHB_dataset)
	Rscript scripts/do_mass2adduct_analysis.R $< 6.048 275 plots/07_Mussel_CHCA3
	pdftk plots/07_*.pdf cat output $@

plots/08_Mussel_CHCA4_combined_plots.pdf: corrtest_Rdata/08_Mussel_CHCA4_no.filter.Rworkspace.Rda $(pure_DHB_dataset)
	Rscript scripts/do_mass2adduct_analysis.R $< 1 155 plots/08_Mussel_CHCA4
	pdftk plots/08_*.pdf cat output $@

plots/09_Brain_Bruker_DHB_combined_plots.pdf: corrtest_Rdata/09_Brain_Bruker_DHB_ppm.filter.Rworkspace.Rda $(pure_DHB_dataset)
	Rscript scripts/do_mass2adduct_analysis.R $< 2.825 0 plots/09_Brain_Bruker_DHB
	pdftk plots/09_*.pdf cat output $@

plots/10_Brain_Thermo_DHB_combined_plots.pdf: corrtest_Rdata/10_Brain_Thermo_DHB_no.filter.Rworkspace.Rda $(pure_DHB_dataset)
	Rscript scripts/do_mass2adduct_analysis.R $< 1 96 plots/10_Brain_Thermo_DHB
	pdftk plots/10_*.pdf cat output $@

plots/11_Brain_MALDI_Waters_DHB_combined_plots.pdf: corrtest_Rdata/11_Brain_MALDI_Waters_DHB_waters.filter.Rworkspace.Rda $(pure_DHB_dataset)
	Rscript scripts/do_mass2adduct_analysis.R $< 5 0 plots/11_Brain_MALDI_Waters_DHB
	pdftk plots/11_*.pdf cat output $@

plots/12_Brain_MALDI2_Waters_DHB_combined_plots.pdf: corrtest_Rdata/12_Brain_MALDI2_Waters_DHB_waters.filter.Rworkspace.Rda $(pure_DHB_dataset)
	Rscript scripts/do_mass2adduct_analysis.R $< 5 0 plots/12_Brain_MALDI2_Waters_DHB
	pdftk plots/12_*.pdf cat output $@

plots/13_Testis_DHB_combined_plots.pdf: corrtest_Rdata/13_Testis_DHB_ppm.filter.Rworkspace.Rda $(pure_DHB_dataset)
	Rscript scripts/do_mass2adduct_analysis.R $< 11.036 0 plots/13_Testis_DHB
	pdftk plots/13_*.pdf cat output $@

plots/14_Cocoa_DHB_combined_plots.pdf: corrtest_Rdata/14_Cocoa_DHB_ppm.filter.Rworkspace.Rda $(pure_DHB_dataset)
	Rscript scripts/do_mass2adduct_analysis.R $< 4.036 0 plots/14_Cocoa_DHB
	pdftk plots/14_*.pdf cat output $@
	
plots15_Seagrass_DHB_combined_plots.pdf: corrtest_Rdata/15_Seagrass_DHB_ppm.filter.Rworkspace.Rda $(pure_DHB_dataset)
	Rscript scripts/do_mass2adduct_analysis.R $< 3.122 250 plots/15_Seagrass_DHB
	pdftk plots/15_*.pdf cat output $@
	
plots/16_Fungus_DHB_combined_plots.pdf: corrtest_Rdata/16_Fungus_DHB_waters.filter.Rworkspace.Rda $(pure_DHB_dataset)
	Rscript scripts/do_mass2adduct_analysis.R $< 5 0 plots/16_Fungus_DHB
	pdftk plots/16_*.pdf cat output $@

plots/17_MetaMix_DHB_combined_plots.pdf: corrtest_Rdata/17_MetaMix_DHB_no.filter.Rworkspace.Rda $(pure_DHB_dataset)
	Rscript scripts/do_mass2adduct_analysis.R $< 1 89 plots/17_MetaMix_DHB
	pdftk plots/17_*.pdf cat output $@

plots/18_MetaMix_CHCA_combined_plots.pdf: corrtest_Rdata/18_MetaMix_CHCA_no.filter.Rworkspace.Rda $(pure_DHB_dataset)
	Rscript scripts/do_mass2adduct_analysis.R $< 1 75 plots/18_MetaMix_CHCA
	pdftk plots/18_*.pdf cat output $@

# Plots after subtracting pure DHB matrix-cluster peaks

plots_pureDHB_subtraction/01_Mussel_DHB1_combined_plots.pdf: corrtest_Rdata/01_Mussel_DHB1_ppm.filter.Rworkspace.Rda $(pure_DHB_dataset)
	Rscript scripts/do_mass2adduct_analysis_pureDHB_subtraction.R $< 2.777 355 plots_pureDHB_subtraction/01_Mussel_DHB1
	pdftk plots_pureDHB_subtraction/01_*.pdf cat output $@

plots_pureDHB_subtraction/02_Mussel_DHB2_combined_plots.pdf: corrtest_Rdata/02_Mussel_DHB2_ppm.filter.Rworkspace.Rda $(pure_DHB_dataset)
	Rscript scripts/do_mass2adduct_analysis_pureDHB_subtraction.R $< 4.115 500 plots_pureDHB_subtraction/02_Mussel_DHB2
	pdftk plots_pureDHB_subtraction/02_*.pdf cat output $@

plots_pureDHB_subtraction/03_Mussel_DHB3_combined_plots.pdf: corrtest_Rdata/03_Mussel_DHB3_ppm.filter.Rworkspace.Rda $(pure_DHB_dataset)
	Rscript scripts/do_mass2adduct_analysis_pureDHB_subtraction.R $< 9.410 315 plots_pureDHB_subtraction/03_Mussel_DHB3
	pdftk plots_pureDHB_subtraction/03_*.pdf cat output $@

plots_pureDHB_subtraction/04_Mussel_DHB4_combined_plots.pdf: corrtest_Rdata/04_Mussel_DHB4_no.filter.Rworkspace.Rda $(pure_DHB_dataset)
	Rscript scripts/do_mass2adduct_analysis_pureDHB_subtraction.R $< 1 150 plots_pureDHB_subtraction/04_Mussel_DHB4
	pdftk plots_pureDHB_subtraction/04_*.pdf cat output $@

plots_pureDHB_subtraction/05_Mussel_CHCA1_combined_plots.pdf: corrtest_Rdata/05_Mussel_CHCA1_ppm.filter.Rworkspace.Rda $(pure_DHB_dataset)
	Rscript scripts/do_mass2adduct_analysis_pureDHB_subtraction.R $< 2 355 plots_pureDHB_subtraction/05_Mussel_CHCA1
	pdftk plots_pureDHB_subtraction/05_*.pdf cat output $@

plots_pureDHB_subtraction/06_Mussel_CHCA2_combined_plots.pdf: corrtest_Rdata/06_Mussel_CHCA2_ppm.filter.Rworkspace.Rda $(pure_DHB_dataset)
	Rscript scripts/do_mass2adduct_analysis_pureDHB_subtraction.R $< 2.554 100 plots_pureDHB_subtraction/06_Mussel_CHCA2
	pdftk plots_pureDHB_subtraction/06_*.pdf cat output $@

plots_pureDHB_subtraction/07_Mussel_CHCA3_combined_plots.pdf: corrtest_Rdata/07_Mussel_CHCA3_ppm.filter.Rworkspace.Rda $(pure_DHB_dataset)
	Rscript scripts/do_mass2adduct_analysis_pureDHB_subtraction.R $< 6.048 275 plots_pureDHB_subtraction/07_Mussel_CHCA3
	pdftk plots_pureDHB_subtraction/07_*.pdf cat output $@

plots_pureDHB_subtraction/08_Mussel_CHCA4_combined_plots.pdf: corrtest_Rdata/08_Mussel_CHCA4_no.filter.Rworkspace.Rda $(pure_DHB_dataset)
	Rscript scripts/do_mass2adduct_analysis_pureDHB_subtraction.R $< 1 155 plots_pureDHB_subtraction/08_Mussel_CHCA4
	pdftk plots_pureDHB_subtraction/08_*.pdf cat output $@

plots_pureDHB_subtraction/09_Brain_Bruker_DHB_combined_plots.pdf: corrtest_Rdata/09_Brain_Bruker_DHB_ppm.filter.Rworkspace.Rda $(pure_DHB_dataset)
	Rscript scripts/do_mass2adduct_analysis_pureDHB_subtraction.R $< 2.825 0 plots_pureDHB_subtraction/09_Brain_Bruker_DHB
	pdftk plots_pureDHB_subtraction/09_*.pdf cat output $@

plots_pureDHB_subtraction/10_Brain_Thermo_DHB_combined_plots.pdf: corrtest_Rdata/10_Brain_Thermo_DHB_no.filter.Rworkspace.Rda $(pure_DHB_dataset)
	Rscript scripts/do_mass2adduct_analysis_pureDHB_subtraction.R $< 1 96 plots_pureDHB_subtraction/10_Brain_Thermo_DHB
	pdftk plots_pureDHB_subtraction/10_*.pdf cat output $@

plots_pureDHB_subtraction/11_Brain_MALDI_Waters_DHB_combined_plots.pdf: corrtest_Rdata/11_Brain_MALDI_Waters_DHB_waters.filter.Rworkspace.Rda $(pure_DHB_dataset)
	Rscript scripts/do_mass2adduct_analysis_pureDHB_subtraction.R $< 0 5 plots_pureDHB_subtraction/11_Brain_MALDI_Waters_DHB
	pdftk plots_pureDHB_subtraction/11_*.pdf cat output $@

plots_pureDHB_subtraction/12_Brain_MALDI2_Waters_DHB_combined_plots.pdf: corrtest_Rdata/12_Brain_MALDI2_Waters_DHB_waters.filter.Rworkspace.Rda $(pure_DHB_dataset)
	Rscript scripts/do_mass2adduct_analysis_pureDHB_subtraction.R $< 0 5 plots_pureDHB_subtraction/12_Brain_MALDI2_Waters_DHB
	pdftk plots_pureDHB_subtraction/12_*.pdf cat output $@

plots_pureDHB_subtraction/13_Testis_DHB_combined_plots.pdf: corrtest_Rdata/13_Testis_DHB_ppm.filter.Rworkspace.Rda $(pure_DHB_dataset)
	Rscript scripts/do_mass2adduct_analysis_pureDHB_subtraction.R $< 11.036 0 plots_pureDHB_subtraction/13_Testis_DHB
	pdftk plots_pureDHB_subtraction/13_*.pdf cat output $@

plots_pureDHB_subtraction/14_Cocoa_DHB_combined_plots.pdf: corrtest_Rdata/14_Cocoa_DHB_ppm.filter.Rworkspace.Rda $(pure_DHB_dataset)
	Rscript scripts/do_mass2adduct_analysis_pureDHB_subtraction.R $< 4.036 0 plots_pureDHB_subtraction/14_Cocoa_DHB
	pdftk plots_pureDHB_subtraction/14_*.pdf cat output $@
	
plots_pureDHB_subtraction15_Seagrass_DHB_combined_plots.pdf: corrtest_Rdata/15_Seagrass_DHB_ppm.filter.Rworkspace.Rda $(pure_DHB_dataset)
	Rscript scripts/do_mass2adduct_analysis_pureDHB_subtraction.R $< 3.122 250 plots_pureDHB_subtraction/15_Seagrass_DHB
	pdftk plots_pureDHB_subtraction/15_*.pdf cat output $@
	
plots_pureDHB_subtraction/16_Fungus_DHB_combined_plots.pdf: corrtest_Rdata/16_Fungus_DHB_waters.filter.Rworkspace.Rda $(pure_DHB_dataset)
	Rscript scripts/do_mass2adduct_analysis_pureDHB_subtraction.R $< 5 0 plots_pureDHB_subtraction/16_Fungus_DHB
	pdftk plots_pureDHB_subtraction/16_*.pdf cat output $@

plots_pureDHB_subtraction/17_MetaMix_DHB_combined_plots.pdf: corrtest_Rdata/17_MetaMix_DHB_no.filter.Rworkspace.Rda $(pure_DHB_dataset)
	Rscript scripts/do_mass2adduct_analysis_pureDHB_subtraction.R $< 1 89 plots_pureDHB_subtraction/17_MetaMix_DHB
	pdftk plots_pureDHB_subtraction/17_*.pdf cat output $@

plots_pureDHB_subtraction/18_MetaMix_CHCA_combined_plots.pdf: corrtest_Rdata/18_MetaMix_CHCA_no.filter.Rworkspace.Rda $(pure_DHB_dataset)
	Rscript scripts/do_mass2adduct_analysis_pureDHB_subtraction.R $< 1 75 plots_pureDHB_subtraction/18_MetaMix_CHCA
	pdftk plots_pureDHB_subtraction/18_*.pdf cat output $@

# Check peak subtraction statistics

peak_subtraction_stats.tsv : $(pure_DHB_dataset)
	Rscript scripts/check_pureDHB_subtraction.R corrtest_Rdata/01_Mussel_DHB1_ppm.filter.Rworkspace.Rda 2.777
	Rscript scripts/check_pureDHB_subtraction.R corrtest_Rdata/02_Mussel_DHB2_ppm.filter.Rworkspace.Rda 4.115
	Rscript scripts/check_pureDHB_subtraction.R corrtest_Rdata/03_Mussel_DHB3_ppm.filter.Rworkspace.Rda 9.410
	Rscript scripts/check_pureDHB_subtraction.R corrtest_Rdata/04_Mussel_DHB4_no.filter.Rworkspace.Rda 1
	Rscript scripts/check_pureDHB_subtraction.R corrtest_Rdata/05_Mussel_CHCA1_ppm.filter.Rworkspace.Rda 2
	Rscript scripts/check_pureDHB_subtraction.R corrtest_Rdata/06_Mussel_CHCA2_ppm.filter.Rworkspace.Rda 2.544
	Rscript scripts/check_pureDHB_subtraction.R corrtest_Rdata/07_Mussel_CHCA3_ppm.filter.Rworkspace.Rda 6.048
	Rscript scripts/check_pureDHB_subtraction.R corrtest_Rdata/08_Mussel_CHCA4_no.filter.Rworkspace.Rda 1
	Rscript scripts/check_pureDHB_subtraction.R corrtest_Rdata/09_Brain_Bruker_DHB_ppm.filter.Rworkspace.Rda 2.825
	Rscript scripts/check_pureDHB_subtraction.R corrtest_Rdata/10_Brain_Thermo_DHB_no.filter.Rworkspace.Rda 1
	Rscript scripts/check_pureDHB_subtraction.R corrtest_Rdata/11_Brain_MALDI_Waters_DHB_waters.filter.Rworkspace.Rda 5
	Rscript scripts/check_pureDHB_subtraction.R corrtest_Rdata/12_Brain_MALDI2_Waters_DHB_waters.filter.Rworkspace.Rda 5
	Rscript scripts/check_pureDHB_subtraction.R corrtest_Rdata/13_Testis_DHB_ppm.filter.Rworkspace.Rda 11.036
	Rscript scripts/check_pureDHB_subtraction.R corrtest_Rdata/14_Cocoa_DHB_ppm.filter.Rworkspace.Rda 4.036
	Rscript scripts/check_pureDHB_subtraction.R corrtest_Rdata/15_Seagrass_DHB_ppm.filter.Rworkspace.Rda 3.122
	Rscript scripts/check_pureDHB_subtraction.R corrtest_Rdata/16_Fungus_DHB_waters.filter.Rworkspace.Rda 5
	Rscript scripts/check_pureDHB_subtraction.R corrtest_Rdata/17_MetaMix_DHB_no.filter.Rworkspace.Rda 1
	Rscript scripts/check_pureDHB_subtraction.R corrtest_Rdata/18_MetaMix_CHCA_no.filter.Rworkspace.Rda 1

## Correlation tests -----------------------------------------------------------

# From triplet files to correlation test results:
# This part was done on HPC server cluster, so not included in Makefile
# Scripts and output are in folder corrtest_Rdata

## Generating input files ------------------------------------------------------

input_files: $(triplets) $(ppm_filter) $(waters_filter) $(no_filter) $(pure_DHB_dataset)

# Conversion to triplet representation
triplets = triplets/01_Mussel_DHB1_ppm.filter_peaknames.list \
triplets/02_Mussel_DHB2_ppm.filter_peaknames.list \
triplets/03_Mussel_DHB3_ppm.filter_peaknames.list \
triplets/04_Mussel_DHB4_no.filter_peaknames.list \
triplets/05_Mussel_CHCA1_ppm.filter_peaknames.list \
triplets/06_Mussel_CHCA2_ppm.filter_peaknames.list \
triplets/07_Mussel_CHCA3_ppm.filter_peaknames.list \
triplets/08_Mussel_CHCA4_no.filter_peaknames.list \
triplets/09_Brain_Bruker_DHB_ppm.filter_peaknames.list \
triplets/10_Brain_Thermo_DHB_no.filter_peaknames.list \
triplets/11_Brain_MALDI_Waters_DHB_waters.filter_peaknames.list \
triplets/12_Brain_MALDI2_Waters_DHB_waters.filter_peaknames.list \
triplets/13_Testis_DHB_ppm.filter_peaknames.list \
triplets/14_Cocoa_DHB_ppm.filter_peaknames.list \
triplets/15_Seagrass_DHB_ppm.filter_peaknames.list \
triplets/16_Fungus_DHB_waters.filter_peaknames.list \
triplets/17_MetaMix_DHB_no.filter_peaknames.list \
triplets/18_MetaMix_CHCA_no.filter_peaknames.list

triplets/%_ppm.filter_peaknames.list: hashimage/%_ppm.filter.hashimage
	FNAME=$(<F); FPREFIX=$${FNAME%%.hashimage}; msimunging.pl --hash $< --outfmt triplet --out $(@D)/$$FPREFIX

triplets/%_waters.filter_peaknames.list: hashimage/%_waters.filter.hashimage
	FNAME=$(<F); FPREFIX=$${FNAME%%.hashimage}; msimunging.pl --hash $< --outfmt triplet --out $(@D)/$$FPREFIX
	
triplets/%_no.filter_peaknames.list: hashimage/%_no.filter.hashimage
	FNAME=$(<F); FPREFIX=$${FNAME%%.hashimage}; msimunging.pl --hash $< --outfmt triplet --out $(@D)/$$FPREFIX

# Peak filtering
ppm_filter = hashimage/01_Mussel_DHB1_ppm.filter.hashimage \
hashimage/02_Mussel_DHB2_ppm.filter.hashimage \
hashimage/03_Mussel_DHB3_ppm.filter.hashimage \
hashimage/05_Mussel_CHCA1_ppm.filter.hashimage \
hashimage/06_Mussel_CHCA2_ppm.filter.hashimage \
hashimage/07_Mussel_CHCA3_ppm.filter.hashimage \
hashimage/09_Brain_Bruker_DHB_ppm.filter.hashimage \
hashimage/13_Testis_DHB_ppm.filter.hashimage \
hashimage/14_Cocoa_DHB_ppm.filter.hashimage \
hashimage/15_Seagrass_DHB_ppm.filter.hashimage

waters_filter = hashimage/11_Brain_MALDI_Waters_DHB_waters.filter.hashimage \
hashimage/12_Brain_MALDI2_Waters_DHB_waters.filter.hashimage \
hashimage/16_Fungus_DHB_waters.filter.hashimage

no_filter = hashimage/04_Mussel_DHB4_no.filter.hashimage \
hashimage/08_Mussel_CHCA4_no.filter.hashimage \
hashimage/10_Brain_Thermo_DHB_no.filter.hashimage \
hashimage/17_MetaMix_DHB_no.filter.hashimage \
hashimage/18_MetaMix_CHCA_no.filter.hashimage

# Waters datasets exported from Waters software
hashimage/%_waters.filter.hashimage: csv_files/%_waters.csv.gz
	GZNAME=$<; CSVNAME=$${GZNAME%%.gz}; \
	gzip -cd $$GZNAME > $$CSVNAME; \
	ONAME=$(@F); OPREFIX=$${ONAME%%.hashimage}; msimunging.pl --delim=", " --crlf --outfmt hashimage --out $$OPREFIX --csv $$CSVNAME; \
	mv $$OPREFIX.hashimage $(@D)
	rm $$CSVNAME

# SCILs exports
hashimage/%_ppm.filter.hashimage: csv_files/%_TIC.csv.gz
	cd $(<D); \
	ONAME=$(@F); OPREFIX=$${ONAME%%.filter.hashimage}; GZNAME=$(<F); CSVNAME=$${GZNAME%%.gz}; \
	gzip -cd $$GZNAME > $$CSVNAME ; msicsvprofiler.pl -skip 10 -delim=", " --crlf --out $$OPREFIX.peakintensity --csv $$CSVNAME;\
	Rscript ../scripts/getFilterPeakList.R $$OPREFIX.peakintensity.tsv 0.0005;\
	msifilterbigcsv.pl --delim=", " --crlf --skip 10 --peaks $$OPREFIX.peakintensity.tsvfilterPeaks.list \
	--out $$OPREFIX.filter --csv $$CSVNAME; rm $$CSVNAME; mv $$OPREFIX.filter.hashimage ../$(@D)/

# Pure matrix compounds
pure_DHB_dataset = triplets/19_Matrix_100_1000_DHB_filter.peaks \
triplets/20_Matrix_500_2000_DHB_filter.peaks

triplets/19_Matrix_100_1000_DHB_filter.peaks: triplets/19_Matrix_100_1000_DHB_peaknames.list
	Rscript do_filter_DHB_peaks.R triplets/19_Matrix_100_1000_DHB 

triplets/20_Matrix_500_2000_DHB_filter.peaks: triplets/20_Matrix_500_2000_DHB_peaknames.list
	Rscript do_filter_DHB_peaks.R triplets/20_Matrix_500_2000_DHB

triplets/19_Matrix_100_1000_DHB_peaknames.list: \
csv_files/19_Matrix_100_1000_DHB.csv\ -\ TIC.csv
	cd $(<D); \
	msimunging.pl --csv $(<F) \
	--outfmt triplet --crlf --skip 10 --delim=", " \
	--out ../../../triplets/19_Matrix_100_1000_DHB

triplets/20_Matrix_500_2000_DHB_peaknames.list: \
csv_files/20_Matrix_500_2000_DHB.csv\ -\ TIC.csv
	cd $(<D); \
	msimunging.pl --csv $(<F) \
	--outfmt triplet --crlf --skip 10 --delim=", " \
	--out ../../../triplets/20_Matrix_500_2000_DHB