Makefile

## Define the versions of R and the paths to the libraries
R := R_LIBS=/home/Shared/Rlib/release-3.4-lib/ /usr/local/R/R-3.3.2/bin/R CMD BATCH --no-restore --no-save
R34 := R_LIBS=/home/Shared/Rlib/release-3.5-lib/ /usr/local/R/R-3.4.0/bin/R CMD BATCH --no-restore --no-save
R34bc36 := R_LIBS=/home/Shared/Rlib/release-3.6-lib/ /usr/local/R/R-3.4.2/bin/R CMD BATCH --no-restore --no-save

## Define paths
cobradir := output/cobra_data
concordancedir := output/concordances
relperfdir := output/relative_performance
realperfdir := output/performance_realtruth
distrdir := output/distribution_fit
figdir := figures
singledsfigdir := figures/single_dataset
multidsfigdir := figures/multi_dataset
dschardir := figures/dataset_characteristics
dstypetxt := data/dataset_type.txt

## Define the active datasets and methods
include include_methods.mk
include plot_methods.mk
include include_datasets.mk
include include_filterings.mk

## Plot types
PLOTTYPE := timing results_characterization results_relativetruth consistency results_relativetruth_all truefpr runfailure  ## done for all data sets
PLOTTYPE1 := timing results_characterization results_relativetruth truefpr runfailure  ## depends on COBRA object
PLOTTYPE2 := consistency  ## depends on COBRA object and concordances
PLOTTYPE3 := results_relativetruth_all  ## depends on relative performances
PLOTTYPE4 := performance_realtruth  ## depends on true performances, only done for simulated signal data sets

## Summary types and corresponding data types where they should be performed
SUMMARYTYPE1 := truefpr crossmethod_consistency orig_vs_mock
SUMMARYTYPE2 := de_characteristics relfprtpr
SUMMARYTYPE3 := fracNA nbrdet
DSTYPE1 := real sim bulk# realdrimpute simdrimpute realscimpute simscimpute realknnsmooth simknnsmooth
DSTYPE2 := real sim# realdrimpute simdrimpute realscimpute simscimpute realknnsmooth simknnsmooth
DSTYPE3 := real bulk# realdrimpute realscimpute realknnsmooth

.PHONY: all

## Define the default rule
all: plotds plotind plotorigmock plotdistr plotprepare plotprepareII cobra diffexp sim \
$(addsuffix _real.rds, $(addprefix $(multidsfigdir)/filtering/summary_filtering_, $(foreach F,$(FILT),$(F)))) \
$(addsuffix _sim.rds, $(addprefix $(multidsfigdir)/filtering/summary_filtering_, $(foreach F,$(FILT),$(F)))) \
$(addsuffix _bulk.rds, $(addprefix $(multidsfigdir)/filtering/summary_filtering_, $(foreach F,$(FILT),$(F)))) \
$(multidsfigdir)/timing/summary_timing_all.rds \
$(multidsfigdir)/runfailure/summary_runfailure_all.rds \
$(multidsfigdir)/tsne/summary_tsne_real.rds \
$(multidsfigdir)/tsne/summary_tsne_sim.rds \
$(multidsfigdir)/pvalhist/summary_pvalhist_real.rds \
$(multidsfigdir)/trueperformance/summary_trueperformance_sim.rds \
$(multidsfigdir)/ds_characteristics/summary_ds_characteristics_real.rds \
$(multidsfigdir)/ds_characteristics/summary_ds_characteristics_sim.rds \
$(multidsfigdir)/ds_characteristics/summary_ds_characteristics_bulk.rds \
$(addsuffix .rds, $(addprefix $(multidsfigdir)/, $(foreach D,$(DSTYPE1),$(foreach S,$(SUMMARYTYPE1),$(S)/summary_$(S)_$(D))))) \
$(addsuffix .rds, $(addprefix $(multidsfigdir)/, $(foreach D,$(DSTYPE2),$(foreach S,$(SUMMARYTYPE2),$(S)/summary_$(S)_$(D))))) \
$(addsuffix .rds, $(addprefix $(multidsfigdir)/, $(foreach D,$(DSTYPE3),$(foreach S,$(SUMMARYTYPE3),$(S)/summary_$(S)_$(D))))) \
figures/misc/voomlimma_investigation.rds figures/misc/performance_summary.rds \
$(multidsfigdir)/crossmethod_consistency/crossmethod_consistency_final_real_100_hclust_annot.rds
#$(multidsfigdir)/trueperformance/summary_trueperformance_simdrimpute.rds \
#$(multidsfigdir)/trueperformance/summary_trueperformance_simscimpute.rds \
#$(multidsfigdir)/trueperformance/summary_trueperformance_simknnsmooth.rds \

## Update data for shiny app
updateshiny: export_results/shiny_results.rds

#decent: $(addsuffix .rds, $(addprefix results/, $(foreach Y,$(DS),$(Y)_DECENT))) \
#$(addsuffix .rds, $(addprefix results/, $(foreach F,$(FILT),$(foreach Y,$(DS),$(Y)_DECENT_$(F)))))

## Plot original vs mock comparison
plotorigmock: $(addsuffix _orig_vs_mock_summary_data.rds, $(addprefix $(figdir)/orig_vs_mock/, $(foreach Y,$(Dsb),$(Y)))) \
$(addsuffix _orig_vs_mock_summary_data.rds, $(addprefix $(figdir)/orig_vs_mock/, $(foreach F,$(FILT),$(foreach Y,$(Dsb),$(Y)_$(F))))) \
$(addsuffix _orig_vs_mock_summary_data.rds, $(addprefix $(figdir)/orig_vs_mock/, $(foreach Y,$(Dsbsim),$(Y)))) \
$(addsuffix _orig_vs_mock_summary_data.rds, $(addprefix $(figdir)/orig_vs_mock/, $(foreach F,$(FILT),$(foreach Y,$(Dsbsim),$(Y)_$(F))))) \
$(addsuffix _orig_vs_mock_summary_data.rds, $(addprefix $(figdir)/orig_vs_mock/, $(foreach Y,$(DSbulksignal),$(Y)))) \
$(addsuffix _orig_vs_mock_summary_data.rds, $(addprefix $(figdir)/orig_vs_mock/, $(foreach F,$(FILT),$(foreach Y,$(DSbulksignal),$(Y)_$(F)))))
#$(addsuffix _orig_vs_mock_summary_data.rds, $(addprefix $(figdir)/orig_vs_mock/, $(foreach Y,$(Dsbscimpute),$(Y)))) \
#$(addsuffix _orig_vs_mock_summary_data.rds, $(addprefix $(figdir)/orig_vs_mock/, $(foreach F,$(FILT),$(foreach Y,$(Dsbscimpute),$(Y)_$(F))))) \
#$(addsuffix _orig_vs_mock_summary_data.rds, $(addprefix $(figdir)/orig_vs_mock/, $(foreach Y,$(Dsbsimscimpute),$(Y)))) \
#$(addsuffix _orig_vs_mock_summary_data.rds, $(addprefix $(figdir)/orig_vs_mock/, $(foreach F,$(FILT),$(foreach Y,$(Dsbsimscimpute),$(Y)_$(F))))) \
#$(addsuffix _orig_vs_mock_summary_data.rds, $(addprefix $(figdir)/orig_vs_mock/, $(foreach Y,$(Dsbdrimpute),$(Y)))) \
#$(addsuffix _orig_vs_mock_summary_data.rds, $(addprefix $(figdir)/orig_vs_mock/, $(foreach F,$(FILT),$(foreach Y,$(Dsbdrimpute),$(Y)_$(F))))) \
#$(addsuffix _orig_vs_mock_summary_data.rds, $(addprefix $(figdir)/orig_vs_mock/, $(foreach Y,$(Dsbsimdrimpute),$(Y)))) \
#$(addsuffix _orig_vs_mock_summary_data.rds, $(addprefix $(figdir)/orig_vs_mock/, $(foreach F,$(FILT),$(foreach Y,$(Dsbsimdrimpute),$(Y)_$(F))))) \
#$(addsuffix _orig_vs_mock_summary_data.rds, $(addprefix $(figdir)/orig_vs_mock/, $(foreach Y,$(Dsbknnsmooth),$(Y)))) \
#$(addsuffix _orig_vs_mock_summary_data.rds, $(addprefix $(figdir)/orig_vs_mock/, $(foreach F,$(FILT),$(foreach Y,$(Dsbknnsmooth),$(Y)_$(F))))) \
#$(addsuffix _orig_vs_mock_summary_data.rds, $(addprefix $(figdir)/orig_vs_mock/, $(foreach Y,$(Dsbsimknnsmooth),$(Y)))) \
#$(addsuffix _orig_vs_mock_summary_data.rds, $(addprefix $(figdir)/orig_vs_mock/, $(foreach F,$(FILT),$(foreach Y,$(Dsbsimknnsmooth),$(Y)_$(F)))))

## Plot individual data set results
plotind: $(addsuffix _summary_data.rds, $(addprefix $(singledsfigdir)/, $(foreach P,$(PLOTTYPE),$(foreach Y,$(DS),$(P)/$(Y)_$(P))))) \
$(addsuffix _summary_data.rds, $(addprefix $(singledsfigdir)/, $(foreach P,$(PLOTTYPE),$(foreach F,$(FILT),$(foreach Y,$(DS),$(P)/$(Y)_$(F)_$(P)))))) \
$(addsuffix _summary_data.rds, $(addprefix $(singledsfigdir)/, $(foreach P,$(PLOTTYPE),$(foreach Y,$(DSbulk),$(P)/$(Y)_$(P))))) \
$(addsuffix _summary_data.rds, $(addprefix $(singledsfigdir)/, $(foreach P,$(PLOTTYPE),$(foreach F,$(FILT),$(foreach Y,$(DSbulk),$(P)/$(Y)_$(F)_$(P)))))) \
$(addsuffix _summary_data.rds, $(addprefix $(singledsfigdir)/, $(foreach P,$(PLOTTYPE4),$(foreach Y,$(DSsimsignal),$(P)/$(Y)_$(P))))) \
$(addsuffix _summary_data.rds, $(addprefix $(singledsfigdir)/, $(foreach P,$(PLOTTYPE4),$(foreach F,$(FILT),$(foreach Y,$(DSsimsignal),$(P)/$(Y)_$(F)_$(P))))))
#$(addsuffix _summary_data.rds, $(addprefix $(singledsfigdir)/, $(foreach P,$(PLOTTYPE4),$(foreach Y,$(DSsimsignalscimpute),$(P)/$(Y)_$(P))))) \
#$(addsuffix _summary_data.rds, $(addprefix $(singledsfigdir)/, $(foreach P,$(PLOTTYPE4),$(foreach F,$(FILT),$(foreach Y,$(DSsimsignalscimpute),$(P)/$(Y)_$(F)_$(P)))))) \
#$(addsuffix _summary_data.rds, $(addprefix $(singledsfigdir)/, $(foreach P,$(PLOTTYPE4),$(foreach Y,$(DSsimsignaldrimpute),$(P)/$(Y)_$(P))))) \
#$(addsuffix _summary_data.rds, $(addprefix $(singledsfigdir)/, $(foreach P,$(PLOTTYPE4),$(foreach F,$(FILT),$(foreach Y,$(DSsimsignaldrimpute),$(P)/$(Y)_$(F)_$(P)))))) \
#$(addsuffix _summary_data.rds, $(addprefix $(singledsfigdir)/, $(foreach P,$(PLOTTYPE4),$(foreach Y,$(DSsimsignalknnsmooth),$(P)/$(Y)_$(P))))) \
#$(addsuffix _summary_data.rds, $(addprefix $(singledsfigdir)/, $(foreach P,$(PLOTTYPE4),$(foreach F,$(FILT),$(foreach Y,$(DSsimsignalknnsmooth),$(P)/$(Y)_$(F)_$(P))))))

## Plot distribution fits
plotdistr: $(addsuffix _distribution_fit_summary_data.rds, $(addprefix $(distrdir)/, $(foreach Y,$(DSrealmock),$(Y)))) \
$(addsuffix _distribution_fit_summary_data.rds, $(addprefix $(distrdir)/, $(foreach F,$(FILT),$(foreach Y,$(DSrealmock),$(Y)_$(F))))) \
$(addsuffix _distribution_fit_summary_data.rds, $(addprefix $(distrdir)/, $(foreach Y,$(DSsimmock),$(Y)))) \
$(addsuffix _distribution_fit_summary_data.rds, $(addprefix $(distrdir)/, $(foreach F,$(FILT),$(foreach Y,$(DSsimmock),$(Y)_$(F))))) \
$(addsuffix _distribution_fit_summary_data.rds, $(addprefix $(distrdir)/, $(foreach Y,$(DSbulkmock),$(Y)))) \
$(addsuffix _distribution_fit_summary_data.rds, $(addprefix $(distrdir)/, $(foreach F,$(FILT),$(foreach Y,$(DSbulkmock),$(Y)_$(F)))))

## Plot data set characteristics
plotds: $(addsuffix _dataset_characteristics_summary_data.rds, $(addprefix $(dschardir)/, $(foreach Y,$(DS),$(Y)))) \
$(addsuffix _dataset_characteristics_summary_data.rds, $(addprefix $(dschardir)/, $(foreach F,$(FILT),$(foreach Y,$(DS),$(Y)_$(F))))) \
$(addsuffix _dataset_characteristics_summary_data.rds, $(addprefix $(dschardir)/, $(foreach Y,$(DSbulk),$(Y)))) \
$(addsuffix _dataset_characteristics_summary_data.rds, $(addprefix $(dschardir)/, $(foreach F,$(FILT),$(foreach Y,$(DSbulk),$(Y)_$(F)))))

## Prepare results for plotting, step II
plotprepare: $(addsuffix _concordances.rds, $(addprefix $(concordancedir)/, $(foreach Y,$(DS),$(Y)))) \
$(addsuffix _concordances.rds, $(addprefix $(concordancedir)/, $(foreach F,$(FILT),$(foreach Y,$(DS),$(Y)_$(F))))) \
$(addsuffix _concordances.rds, $(addprefix $(concordancedir)/, $(foreach Y,$(DSbulk),$(Y)))) \
$(addsuffix _concordances.rds, $(addprefix $(concordancedir)/, $(foreach F,$(FILT),$(foreach Y,$(DSbulk),$(Y)_$(F))))) \
$(addsuffix _relative_performance.rds, $(addprefix $(relperfdir)/, $(foreach Y,$(DS),$(Y)))) \
$(addsuffix _relative_performance.rds, $(addprefix $(relperfdir)/, $(foreach F,$(FILT),$(foreach Y,$(DS),$(Y)_$(F))))) \
$(addsuffix _relative_performance.rds, $(addprefix $(relperfdir)/, $(foreach Y,$(DSbulk),$(Y)))) \
$(addsuffix _relative_performance.rds, $(addprefix $(relperfdir)/, $(foreach F,$(FILT),$(foreach Y,$(DSbulk),$(Y)_$(F)))))

plotprepareII: $(addsuffix _performance.rds, $(addprefix $(realperfdir)/, $(foreach Y,$(DSsimsignal),$(Y)))) \
$(addsuffix _performance.rds, $(addprefix $(realperfdir)/, $(foreach F,$(FILT),$(foreach Y,$(DSsimsignal),$(Y)_$(F)))))
#$(addsuffix _performance.rds, $(addprefix $(realperfdir)/, $(foreach Y,$(DSsimsignalscimpute),$(Y)))) \
#$(addsuffix _performance.rds, $(addprefix $(realperfdir)/, $(foreach F,$(FILT),$(foreach Y,$(DSsimsignalscimpute),$(Y)_$(F))))) \
#$(addsuffix _performance.rds, $(addprefix $(realperfdir)/, $(foreach Y,$(DSsimsignaldrimpute),$(Y)))) \
#$(addsuffix _performance.rds, $(addprefix $(realperfdir)/, $(foreach F,$(FILT),$(foreach Y,$(DSsimsignaldrimpute),$(Y)_$(F))))) \
#$(addsuffix _performance.rds, $(addprefix $(realperfdir)/, $(foreach Y,$(DSsimsignalknnsmooth),$(Y)))) \
#$(addsuffix _performance.rds, $(addprefix $(realperfdir)/, $(foreach F,$(FILT),$(foreach Y,$(DSsimsignalknnsmooth),$(Y)_$(F)))))

## Prepare results for plotting, step I
cobra: $(addsuffix _cobra.rds, $(addprefix $(cobradir)/, $(foreach Y,$(DS),$(Y)))) \
$(addsuffix _cobra.rds, $(addprefix $(cobradir)/, $(foreach F,$(FILT),$(foreach Y,$(DS),$(Y)_$(F))))) \
$(addsuffix _cobra.rds, $(addprefix $(cobradir)/, $(foreach Y,$(DSbulk),$(Y)))) \
$(addsuffix _cobra.rds, $(addprefix $(cobradir)/, $(foreach F,$(FILT),$(foreach Y,$(DSbulk),$(Y)_$(F)))))

## Run differential expression
diffexp: $(addsuffix .rds, $(addprefix results/, $(foreach M,$(MT),$(foreach Y,$(DS),$(Y)_$(M))))) \
$(addsuffix .rds, $(addprefix results/, $(foreach F,$(FILT),$(foreach M,$(MT),$(foreach Y,$(DS),$(Y)_$(M)_$(F)))))) \
$(addsuffix .rds, $(addprefix results/, $(foreach M,$(MTbulk),$(foreach Y,$(DSbulk),$(Y)_$(M))))) \
$(addsuffix .rds, $(addprefix results/, $(foreach F,$(FILT),$(foreach M,$(MTbulk),$(foreach Y,$(DSbulk),$(Y)_$(M)_$(F))))))

## List all packages
listpackages:
	$(R) scripts/list_packages.R Rout/list_packages.Rout

## Simulate data
sim: $(addsuffix .rds, $(addprefix data/, $(foreach Y,$(DSforsim),$(Y)sim123))) \
$(addsuffix .rds, $(addprefix data/, $(foreach Y,$(DSforsim),$(Y)sim123mock)))

## List all rules
list:
	@$(MAKE) -pRrq -f $(lastword $(MAKEFILE_LIST)) : 2>/dev/null | awk -v RS= -F: '/^# File/,/^# Finished Make data base/ {if ($$1 !~ "^[#.]") {print $$1}}' | sort | egrep -v -e '^[^[:alnum:]]' -e '^$@$$' | xargs

## Make sure no intermediate files are deleted
.SECONDARY:

## ------------------------ Dependencies between R scripts ---------------------------- ##
## ------------------------------------------------------------------------------------ ##
scripts/calculate_concordances.R: scripts/concordance_functions.R
	touch $@
	
scripts/investigate_voomlimma_results.R: scripts/prepare_mae.R
	touch $@
	
scripts/plot_setup.R: scripts/prepare_mae.R
	touch $@
	
scripts/plot_single_dataset_consistency.R: scripts/help_function_crossmethod_concordance.R
	touch $@
	
scripts/prepare_cobra_for_evaluation.R: scripts/prepare_mae.R scripts/calculate_gene_characteristics.R
	touch $@
	
scripts/run_diffexpression.R: scripts/prepare_mae.R
	touch $@

scripts/run_distribution_fit.R: scripts/prepare_mae.R
	touch $@
	
scripts/run_plot_dataset_characterization.R: scripts/prepare_mae.R scripts/calculate_gene_characteristics.R scripts/calculate_cell_characteristics.R
	touch $@
	
scripts/run_plot_multi_dataset_summarization.R: scripts/plot_setup.R $(dstypetxt) 
	touch $@
	
scripts/run_plot_single_dataset_evaluation.R: scripts/plot_setup.R
	touch $@
	
scripts/run_plot_single_dataset_origvsmock.R: scripts/plot_setup.R scripts/plot_single_dataset_origvsmock.R
	touch $@
	
scripts/simulate_data.R: scripts/powsim_modified_functions.R
	touch $@
	
scripts/summarize_crossmethod_consistency.R: scripts/help_function_crossmethod_concordance.R
	touch $@

## -------------------------- Generate configuration files ---------------------------- ##
## ------------------------------------------------------------------------------------ ##
define configrule
config/$(1).json: scripts/generate_config_$(1).R
	mkdir -p config
	$(R) scripts/generate_config_$(1).R Rout/generate_config_$(1).Rout
endef
$(foreach Y,$(DS),$(eval $(call configrule,$(Y))))
$(foreach Y,$(DSbulk),$(eval $(call configrule,$(Y))))

## --------------------------------- Simulate data ------------------------------------ ##
## ------------------------------------------------------------------------------------ ##
define simrule
data/$(1)sim$(2).rds: scripts/simulate_data.R data/$(1).rds config/$(1).json 
	mkdir -p data
	$(R) "--args dataset='$(1)' config_file='config/$(1).json' pDE=0.1 seed=$(2)" scripts/simulate_data.R Rout/simulate_data_$(1)_$(2).Rout
endef
$(foreach Y,$(DSforsim),$(eval $(call simrule,$(Y),123)))

define simruletruth
data/$(1)sim$(2)_truth.rds: data/$(1)sim$(2).rds
	
endef
$(foreach Y,$(DSforsim),$(eval $(call simruletruth,$(Y),123)))

define simrulemock
data/$(1)sim$(2)mock.rds: data/$(1)sim$(2).rds
	scp data/$(1)sim$(2).rds data/$(1)sim$(2)mock.rds
endef
$(foreach Y,$(DSforsim),$(eval $(call simrulemock,$(Y),123)))

#data/GSE74596sim123scimpute.rds: data/GSE74596sim123.rds
#	scp $< $@

#data/GSE74596sim123scimpute_truth.rds: data/GSE74596sim123_truth.rds
#	scp $< $@

#data/GSE74596sim123scimputemock.rds: data/GSE74596sim123mock.rds
#	scp $< $@

#data/GSE74596sim123drimpute.rds: data/GSE74596sim123.rds
#	scp $< $@

#data/GSE74596sim123drimpute_truth.rds: data/GSE74596sim123_truth.rds
#	scp $< $@

#data/GSE74596sim123drimputemock.rds: data/GSE74596sim123mock.rds
#	scp $< $@

#data/GSE74596sim123knnsmooth.rds: data/GSE74596sim123.rds
#	scp $< $@

#data/GSE74596sim123knnsmooth_truth.rds: data/GSE74596sim123_truth.rds
#	scp $< $@

#data/GSE74596sim123knnsmoothmock.rds: data/GSE74596sim123mock.rds
#	scp $< $@

## ------------------------------- Imputed data sets ---------------------------------- ##
## ------------------------------------------------------------------------------------ ##
#data/GSE74596knnsmooth.rds: data/GSE74596.rds
#	scp $< $@

#data/GSE74596knnsmoothmock.rds: data/GSE74596mock.rds
#	scp $< $@

## --------------------------- Extract sample subsets --------------------------------- ##
## ------------------------------------------------------------------------------------ ##
define subsetrule
subsets/$(1)_subsets.rds: data/$(1).rds config/$(1).json scripts/generate_subsets.R
	mkdir -p subsets
	$(R) "--args config_file='config/$(1).json'" scripts/generate_subsets.R Rout/generate_subsets_$(1).Rout
endef
$(foreach Y,$(DS),$(eval $(call subsetrule,$(Y))))
$(foreach Y,$(DSbulk),$(eval $(call subsetrule,$(Y))))

## -------------------------- Generate Usoskin data set ------------------------------- ##
## ------------------------------------------------------------------------------------ ##
data/UsoskinGSE59739.rds: scripts/generate_Usoskin_mae.R data/Usoskin_External_resources_Table_1.txt
	$(R) scripts/generate_Usoskin_mae.R Rout/generate_Usoskin_mae.Rout

## --------------------- Generate GSE62270-GPL17021 data set -------------------------- ##
## ------------------------------------------------------------------------------------ ##
data/GSE62270-GPL17021.rds: scripts/generate_GSE62270_mae.R data/GSE62270-GPL17021-orig.rds
	$(R) scripts/generate_GSE62270_mae.R Rout/generate_GSE62270_mae.Rout

data/GSE62270-GPL17021mock.rds: data/GSE62270-GPL17021.rds

## ------------------------ Generate 10XMonoCytoT data set ---------------------------- ##
## ------------------------------------------------------------------------------------ ##
data/10XMonoCytoT.rds: scripts/generate_10XMonoCytoT_mae.R data/10xGenomics/cd14_monocytes_matrices_mex/hg19/barcodes.tsv \
data/10xGenomics/cd14_monocytes_matrices_mex/hg19/genes.tsv data/10xGenomics/cd14_monocytes_matrices_mex/hg19/matrix.mtx \
data/10xGenomics/cytotoxic_t_matrices_mex/hg19/barcodes.tsv data/10xGenomics/cytotoxic_t_matrices_mex/hg19/genes.tsv \
data/10xGenomics/cytotoxic_t_matrices_mex/hg19/matrix.mtx
	$(R) scripts/generate_10XMonoCytoT_mae.R Rout/generate_10XMonoCytoT_mae.Rout

data/10XMonoCytoTmock.rds: data/10XMonoCytoT.rds
	
## ------------------ Define rules for differential expression ------------------------ ##
## ------------------------------------------------------------------------------------ ##
define dgerule3.3
results/$(1)_$(2)$(4).rds: scripts/apply_$(2).R \
scripts/run_diffexpression.R subsets/$(1)_subsets.rds data/$(1).rds
	mkdir -p results
	$(R) "--args config_file='config/$(1).json' demethod='$(2)' filt='$(3)'" scripts/run_diffexpression.R Rout/run_diffexpression_$(1)_$(2)$(4).Rout
endef
$(foreach M,$(MT3.3),$(foreach Y,$(DSnonimpute),$(eval $(call dgerule3.3,$(Y),$(M),,))))
$(foreach M,$(MTbulk),$(foreach Y,$(DSbulk),$(eval $(call dgerule3.3,$(Y),$(M),,))))
$(foreach F,$(FILT),$(foreach M,$(MT3.3),$(foreach Y,$(DSnonimpute),$(eval $(call dgerule3.3,$(Y),$(M),$(F),_$(F))))))
$(foreach F,$(FILT),$(foreach M,$(MTbulk),$(foreach Y,$(DSbulk),$(eval $(call dgerule3.3,$(Y),$(M),$(F),_$(F))))))
## DESeq2 with betaPrior = FALSE, for GSE62270 data set
#$(eval $(call dgerule3.3,GSE62270-GPL17021,DESeq2betapFALSE,,))

#define dgerule3.3scimpute
#results/$(1)_$(2)$(4).rds: scripts/apply_$(2).R \
#scripts/run_diffexpression.R subsets/$(1)_subsets.rds data/$(1).rds scripts/scimpute_dropouts.R
#	mkdir -p results
#	$(R) "--args config_file='config/$(1).json' demethod='$(2)' filt='$(3)'" scripts/run_diffexpression.R Rout/run_diffexpression_$(1)_$(2)$(4).Rout
#endef
#$(foreach M,$(MT3.3),$(foreach Y,$(DSscimpute),$(eval $(call dgerule3.3scimpute,$(Y),$(M),,))))
#$(foreach F,$(FILT),$(foreach M,$(MT3.3),$(foreach Y,$(DSscimpute),$(eval $(call dgerule3.3scimpute,$(Y),$(M),$(F),_$(F))))))

#define dgerule3.3drimpute
#results/$(1)_$(2)$(4).rds: scripts/apply_$(2).R \
#scripts/run_diffexpression.R subsets/$(1)_subsets.rds data/$(1).rds scripts/drimpute_dropouts.R
#	mkdir -p results
#	$(R) "--args config_file='config/$(1).json' demethod='$(2)' filt='$(3)'" scripts/run_diffexpression.R Rout/run_diffexpression_$(1)_$(2)$(4).Rout
#endef
#$(foreach M,$(MT3.3),$(foreach Y,$(DSdrimpute),$(eval $(call dgerule3.3drimpute,$(Y),$(M),,))))
#$(foreach F,$(FILT),$(foreach M,$(MT3.3),$(foreach Y,$(DSdrimpute),$(eval $(call dgerule3.3drimpute,$(Y),$(M),$(F),_$(F))))))

#define dgerule3.3knnsmooth
#results/$(1)_$(2)$(4).rds: scripts/apply_$(2).R \
#scripts/run_diffexpression.R subsets/$(1)_subsets.rds data/$(1).rds scripts/knnsmooth_dropouts.R
#	mkdir -p results
#	$(R) "--args config_file='config/$(1).json' demethod='$(2)' filt='$(3)'" scripts/run_diffexpression.R Rout/run_diffexpression_$(1)_$(2)$(4).Rout
#endef
#$(foreach M,$(MT3.3),$(foreach Y,$(DSknnsmooth),$(eval $(call dgerule3.3knnsmooth,$(Y),$(M),,))))
#$(foreach F,$(FILT),$(foreach M,$(MT3.3),$(foreach Y,$(DSknnsmooth),$(eval $(call dgerule3.3knnsmooth,$(Y),$(M),$(F),_$(F))))))


define dgerule3.4
results/$(1)_$(2)$(4).rds: scripts/apply_$(2).R \
scripts/run_diffexpression.R subsets/$(1)_subsets.rds data/$(1).rds
	mkdir -p results
	$(5) "--args config_file='config/$(1).json' demethod='$(2)' filt='$(3)'" scripts/run_diffexpression.R Rout/run_diffexpression_$(1)_$(2)$(4).Rout
endef
$(foreach M,$(MT3.4),$(foreach Y,$(DSnonimpute),$(eval $(call dgerule3.4,$(Y),$(M),,,$(R34)))))
$(foreach F,$(FILT),$(foreach M,$(MT3.4),$(foreach Y,$(DSnonimpute),$(eval $(call dgerule3.4,$(Y),$(M),$(F),_$(F),$(R34))))))
$(foreach M,$(MT3.4bc3.6),$(foreach Y,$(DSnonimpute),$(eval $(call dgerule3.4,$(Y),$(M),,,$(R34bc36)))))
$(foreach F,$(FILT),$(foreach M,$(MT3.4bc3.6),$(foreach Y,$(DSnonimpute),$(eval $(call dgerule3.4,$(Y),$(M),$(F),_$(F),$(R34bc36))))))
## DESeq2 devel, for GSE62270 data set
$(eval $(call dgerule3.4,GSE62270-GPL17021,DESeq2devel,,,$(R34bc36)))
## DECENT
#$(foreach Y,$(DSnonimpute),$(eval $(call dgerule3.4,$(Y),DECENT,,,$(R34bc36))))
#$(foreach F,$(FILT),$(foreach Y,$(DSnonimpute),$(eval $(call dgerule3.4,$(Y),DECENT,$(F),_$(F),$(R34bc36)))))

#define dgerule3.4scimpute
#results/$(1)_$(2)$(4).rds: scripts/apply_$(2).R \
#scripts/run_diffexpression.R subsets/$(1)_subsets.rds data/$(1).rds scripts/scimpute_dropouts.R
#	mkdir -p results
#	$(5) "--args config_file='config/$(1).json' demethod='$(2)' filt='$(3)'" scripts/run_diffexpression.R Rout/run_diffexpression_$(1)_$(2)$(4).Rout
#endef
#$(foreach M,$(MT3.4),$(foreach Y,$(DSscimpute),$(eval $(call dgerule3.4scimpute,$(Y),$(M),,,$(R34)))))
#$(foreach F,$(FILT),$(foreach M,$(MT3.4),$(foreach Y,$(DSscimpute),$(eval $(call dgerule3.4scimpute,$(Y),$(M),$(F),_$(F),$(R34))))))
#$(foreach M,$(MT3.4bc3.6),$(foreach Y,$(DSscimpute),$(eval $(call dgerule3.4scimpute,$(Y),$(M),,,$(R34bc36)))))
#$(foreach F,$(FILT),$(foreach M,$(MT3.4bc3.6),$(foreach Y,$(DSscimpute),$(eval $(call dgerule3.4scimpute,$(Y),$(M),$(F),_$(F),$(R34bc36))))))
## DECENT
#$(foreach Y,$(DSscimpute),$(eval $(call dgerule3.4scimpute,$(Y),DECENT,,,$(R34bc36))))
#$(foreach F,$(FILT),$(foreach Y,$(DSscimpute),$(eval $(call dgerule3.4scimpute,$(Y),DECENT,$(F),_$(F),$(R34bc36)))))

#define dgerule3.4drimpute
#results/$(1)_$(2)$(4).rds: scripts/apply_$(2).R \
#scripts/run_diffexpression.R subsets/$(1)_subsets.rds data/$(1).rds scripts/drimpute_dropouts.R
#	mkdir -p results
#	$(5) "--args config_file='config/$(1).json' demethod='$(2)' filt='$(3)'" scripts/run_diffexpression.R Rout/run_diffexpression_$(1)_$(2)$(4).Rout
#endef
#$(foreach M,$(MT3.4),$(foreach Y,$(DSdrimpute),$(eval $(call dgerule3.4drimpute,$(Y),$(M),,,$(R34)))))
#$(foreach F,$(FILT),$(foreach M,$(MT3.4),$(foreach Y,$(DSdrimpute),$(eval $(call dgerule3.4drimpute,$(Y),$(M),$(F),_$(F),$(R34))))))
#$(foreach M,$(MT3.4bc3.6),$(foreach Y,$(DSdrimpute),$(eval $(call dgerule3.4drimpute,$(Y),$(M),,,$(R34bc36)))))
#$(foreach F,$(FILT),$(foreach M,$(MT3.4bc3.6),$(foreach Y,$(DSdrimpute),$(eval $(call dgerule3.4drimpute,$(Y),$(M),$(F),_$(F),$(R34bc36))))))
## DECENT
#$(foreach Y,$(DSdrimpute),$(eval $(call dgerule3.4drimpute,$(Y),DECENT,,,$(R34bc36))))
#$(foreach F,$(FILT),$(foreach Y,$(DSdrimpute),$(eval $(call dgerule3.4drimpute,$(Y),DECENT,$(F),_$(F),$(R34bc36)))))

#define dgerule3.4knnsmooth
#results/$(1)_$(2)$(4).rds: scripts/apply_$(2).R \
#scripts/run_diffexpression.R subsets/$(1)_subsets.rds data/$(1).rds scripts/knnsmooth_dropouts.R
#	mkdir -p results
#	$(5) "--args config_file='config/$(1).json' demethod='$(2)' filt='$(3)'" scripts/run_diffexpression.R Rout/run_diffexpression_$(1)_$(2)$(4).Rout
#endef
#$(foreach M,$(MT3.4),$(foreach Y,$(DSknnsmooth),$(eval $(call dgerule3.4knnsmooth,$(Y),$(M),,,$(R34)))))
#$(foreach F,$(FILT),$(foreach M,$(MT3.4),$(foreach Y,$(DSknnsmooth),$(eval $(call dgerule3.4knnsmooth,$(Y),$(M),$(F),_$(F),$(R34))))))
#$(foreach M,$(MT3.4bc3.6),$(foreach Y,$(DSknnsmooth),$(eval $(call dgerule3.4knnsmooth,$(Y),$(M),,,$(R34bc36)))))
#$(foreach F,$(FILT),$(foreach M,$(MT3.4bc3.6),$(foreach Y,$(DSknnsmooth),$(eval $(call dgerule3.4knnsmooth,$(Y),$(M),$(F),_$(F),$(R34bc36))))))

## ------------------ Prepare COBRAData object for evaluation ------------------------- ##
## ------------------------------------------------------------------------------------ ##
define cobrarulemock
$(cobradir)/$(1)$(3)_cobra.rds: scripts/prepare_cobra_for_evaluation.R \
$(addsuffix $(3).rds, $(addprefix results/$(1)_, $(foreach M,$(4),$(M)))) include_methods.mk \
$(distrdir)/$(1)$(3)_distribution_fit_summary_data.rds
	mkdir -p $(cobradir)
	$(R) "--args demethods='$(5)' dataset='$(1)' config_file='config/$(1).json' filt='$(2)' resdir='results' distrdir='$(distrdir)' outdir='$(cobradir)'" scripts/prepare_cobra_for_evaluation.R Rout/prepare_cobra_for_evaluation_$(1)$(3)$(6).Rout
endef
$(foreach Y,$(DSrealmock),$(eval $(call cobrarulemock,$(Y),,,$(MT),${MTc},)))
$(foreach Y,$(DSsimmock),$(eval $(call cobrarulemock,$(Y),,,$(MT),${MTc},)))
$(foreach Y,$(DSbulkmock),$(eval $(call cobrarulemock,$(Y),,,$(MTbulk),${MTcbulk},_bulk)))
$(foreach F,$(FILT),$(foreach Y,$(DSrealmock),$(eval $(call cobrarulemock,$(Y),$(F),_$(F),$(MT),${MTc},))))
$(foreach F,$(FILT),$(foreach Y,$(DSsimmock),$(eval $(call cobrarulemock,$(Y),$(F),_$(F),$(MT),${MTc},))))
$(foreach F,$(FILT),$(foreach Y,$(DSbulkmock),$(eval $(call cobrarulemock,$(Y),$(F),_$(F),$(MTbulk),${MTcbulk},_bulk))))

define cobrarulesignal
$(cobradir)/$(1)$(3)_cobra.rds: scripts/prepare_cobra_for_evaluation.R \
$(addsuffix $(3).rds, $(addprefix results/$(1)_, $(foreach M,$(4),$(M)))) include_methods.mk
	mkdir -p $(cobradir)
	$(R) "--args demethods='$(5)' dataset='$(1)' config_file='config/$(1).json' filt='$(2)' resdir='results' distrdir='$(distrdir)' outdir='$(cobradir)'" scripts/prepare_cobra_for_evaluation.R Rout/prepare_cobra_for_evaluation_$(1)$(3)$(6).Rout
endef
$(foreach Y,$(DSrealsignal),$(eval $(call cobrarulesignal,$(Y),,,$(MT),${MTc},)))
$(foreach Y,$(DSsimsignal),$(eval $(call cobrarulesignal,$(Y),,,$(MT),${MTc},)))
$(foreach Y,$(DSbulksignal),$(eval $(call cobrarulesignal,$(Y),,,$(MTbulk),${MTcbulk},_bulk)))
$(foreach F,$(FILT),$(foreach Y,$(DSrealsignal),$(eval $(call cobrarulesignal,$(Y),$(F),_$(F),$(MT),${MTc},))))
$(foreach F,$(FILT),$(foreach Y,$(DSsimsignal),$(eval $(call cobrarulesignal,$(Y),$(F),_$(F),$(MT),${MTc},))))
$(foreach F,$(FILT),$(foreach Y,$(DSbulksignal),$(eval $(call cobrarulesignal,$(Y),$(F),_$(F),$(MTbulk),${MTcbulk},_bulk))))


#define cobrarulescimputesignal
#$(cobradir)/$(1)$(3)_cobra.rds: scripts/prepare_cobra_for_evaluation.R \
#$(addsuffix $(3).rds, $(addprefix results/$(1)_, $(foreach M,$(4),$(M)))) include_methods.mk scripts/scimpute_dropouts.R
#	mkdir -p $(cobradir)
#	$(R) "--args demethods='$(5)' dataset='$(1)' config_file='config/$(1).json' filt='$(2)' resdir='results' distrdir='$(distrdir)' outdir='$(cobradir)'" scripts/prepare_cobra_for_evaluation.R Rout/prepare_cobra_for_evaluation_$(1)$(3)$(6).Rout
#endef
#$(foreach Y,$(DSrealsignalscimpute),$(eval $(call cobrarulescimputesignal,$(Y),,,$(MT),${MTc},)))
#$(foreach Y,$(DSsimsignalscimpute),$(eval $(call cobrarulescimputesignal,$(Y),,,$(MT),${MTc},)))
#$(foreach F,$(FILT),$(foreach Y,$(DSrealsignalscimpute),$(eval $(call cobrarulescimputesignal,$(Y),$(F),_$(F),$(MT),${MTc},))))
#$(foreach F,$(FILT),$(foreach Y,$(DSsimsignalscimpute),$(eval $(call cobrarulescimputesignal,$(Y),$(F),_$(F),$(MT),${MTc},))))

#define cobrarulescimputemock
#$(cobradir)/$(1)$(3)_cobra.rds: scripts/prepare_cobra_for_evaluation.R \
#$(addsuffix $(3).rds, $(addprefix results/$(1)_, $(foreach M,$(4),$(M)))) include_methods.mk scripts/scimpute_dropouts.R
#	mkdir -p $(cobradir)
#	$(R) "--args demethods='$(5)' dataset='$(1)' config_file='config/$(1).json' filt='$(2)' resdir='results' distrdir='$(distrdir)' outdir='$(cobradir)'" scripts/prepare_cobra_for_evaluation.R Rout/prepare_cobra_for_evaluation_$(1)$(3)$(6).Rout
#endef
#$(foreach Y,$(DSrealmockscimpute),$(eval $(call cobrarulescimputemock,$(Y),,,$(MT),${MTc},)))
#$(foreach Y,$(DSsimmockscimpute),$(eval $(call cobrarulescimputemock,$(Y),,,$(MT),${MTc},)))
#$(foreach F,$(FILT),$(foreach Y,$(DSrealmockscimpute),$(eval $(call cobrarulescimputemock,$(Y),$(F),_$(F),$(MT),${MTc},))))
#$(foreach F,$(FILT),$(foreach Y,$(DSsimmockscimpute),$(eval $(call cobrarulescimputemock,$(Y),$(F),_$(F),$(MT),${MTc},))))


#define cobraruledrimputesignal
#$(cobradir)/$(1)$(3)_cobra.rds: scripts/prepare_cobra_for_evaluation.R \
#$(addsuffix $(3).rds, $(addprefix results/$(1)_, $(foreach M,$(4),$(M)))) include_methods.mk scripts/drimpute_dropouts.R
#	mkdir -p $(cobradir)
#	$(R) "--args demethods='$(5)' dataset='$(1)' config_file='config/$(1).json' filt='$(2)' resdir='results' distrdir='$(distrdir)' outdir='$(cobradir)'" scripts/prepare_cobra_for_evaluation.R Rout/prepare_cobra_for_evaluation_$(1)$(3)$(6).Rout
#endef
#$(foreach Y,$(DSrealsignaldrimpute),$(eval $(call cobraruledrimputesignal,$(Y),,,$(MT),${MTc},)))
#$(foreach Y,$(DSsimsignaldrimpute),$(eval $(call cobraruledrimputesignal,$(Y),,,$(MT),${MTc},)))
#$(foreach F,$(FILT),$(foreach Y,$(DSrealsignaldrimpute),$(eval $(call cobraruledrimputesignal,$(Y),$(F),_$(F),$(MT),${MTc},))))
#$(foreach F,$(FILT),$(foreach Y,$(DSsimsignaldrimpute),$(eval $(call cobraruledrimputesignal,$(Y),$(F),_$(F),$(MT),${MTc},))))

#define cobraruledrimputemock
#$(cobradir)/$(1)$(3)_cobra.rds: scripts/prepare_cobra_for_evaluation.R \
#$(addsuffix $(3).rds, $(addprefix results/$(1)_, $(foreach M,$(4),$(M)))) include_methods.mk scripts/drimpute_dropouts.R
#	mkdir -p $(cobradir)
#	$(R) "--args demethods='$(5)' dataset='$(1)' config_file='config/$(1).json' filt='$(2)' resdir='results' distrdir='$(distrdir)' outdir='$(cobradir)'" scripts/prepare_cobra_for_evaluation.R Rout/prepare_cobra_for_evaluation_$(1)$(3)$(6).Rout
#endef
#$(foreach Y,$(DSrealmockdrimpute),$(eval $(call cobraruledrimputemock,$(Y),,,$(MT),${MTc},)))
#$(foreach Y,$(DSsimmockdrimpute),$(eval $(call cobraruledrimputemock,$(Y),,,$(MT),${MTc},)))
#$(foreach F,$(FILT),$(foreach Y,$(DSrealmockdrimpute),$(eval $(call cobraruledrimputemock,$(Y),$(F),_$(F),$(MT),${MTc},))))
#$(foreach F,$(FILT),$(foreach Y,$(DSsimmockdrimpute),$(eval $(call cobraruledrimputemock,$(Y),$(F),_$(F),$(MT),${MTc},))))


#define cobraruleknnsmoothsignal
#$(cobradir)/$(1)$(3)_cobra.rds: scripts/prepare_cobra_for_evaluation.R \
#$(addsuffix $(3).rds, $(addprefix results/$(1)_, $(foreach M,$(4),$(M)))) include_methods.mk scripts/knnsmooth_dropouts.R
#	mkdir -p $(cobradir)
#	$(R) "--args demethods='$(5)' dataset='$(1)' config_file='config/$(1).json' filt='$(2)' resdir='results' distrdir='$(distrdir)' outdir='$(cobradir)'" scripts/prepare_cobra_for_evaluation.R Rout/prepare_cobra_for_evaluation_$(1)$(3)$(6).Rout
#endef
#$(foreach Y,$(DSrealsignalknnsmooth),$(eval $(call cobraruleknnsmoothsignal,$(Y),,,$(MT),${MTc},)))
#$(foreach Y,$(DSsimsignalknnsmooth),$(eval $(call cobraruleknnsmoothsignal,$(Y),,,$(MT),${MTc},)))
#$(foreach F,$(FILT),$(foreach Y,$(DSrealsignalknnsmooth),$(eval $(call cobraruleknnsmoothsignal,$(Y),$(F),_$(F),$(MT),${MTc},))))
#$(foreach F,$(FILT),$(foreach Y,$(DSsimsignalknnsmooth),$(eval $(call cobraruleknnsmoothsignal,$(Y),$(F),_$(F),$(MT),${MTc},))))

#define cobraruleknnsmoothmock
#$(cobradir)/$(1)$(3)_cobra.rds: scripts/prepare_cobra_for_evaluation.R \
#$(addsuffix $(3).rds, $(addprefix results/$(1)_, $(foreach M,$(4),$(M)))) include_methods.mk scripts/knnsmooth_dropouts.R
#	mkdir -p $(cobradir)
#	$(R) "--args demethods='$(5)' dataset='$(1)' config_file='config/$(1).json' filt='$(2)' resdir='results' distrdir='$(distrdir)' outdir='$(cobradir)'" scripts/prepare_cobra_for_evaluation.R Rout/prepare_cobra_for_evaluation_$(1)$(3)$(6).Rout
#endef
#$(foreach Y,$(DSrealmockknnsmooth),$(eval $(call cobraruleknnsmoothmock,$(Y),,,$(MT),${MTc},)))
#$(foreach Y,$(DSsimmockknnsmooth),$(eval $(call cobraruleknnsmoothmock,$(Y),,,$(MT),${MTc},)))
#$(foreach F,$(FILT),$(foreach Y,$(DSrealmockknnsmooth),$(eval $(call cobraruleknnsmoothmock,$(Y),$(F),_$(F),$(MT),${MTc},))))
#$(foreach F,$(FILT),$(foreach Y,$(DSsimmockknnsmooth),$(eval $(call cobraruleknnsmoothmock,$(Y),$(F),_$(F),$(MT),${MTc},))))

## ----------------------------- Calculate concordances ------------------------------- ##
## ------------------------------------------------------------------------------------ ##
define concrule
$(concordancedir)/$(1)$(3)_concordances.rds: scripts/calculate_concordances.R $(cobradir)/$(1)$(3)_cobra.rds 
	mkdir -p $(concordancedir)
	$(R) "--args dataset='$(1)' filt='$(2)' cobradir='$(cobradir)' outdir='$(concordancedir)'" scripts/calculate_concordances.R Rout/calculate_concordances_$(1)$(3).Rout
endef
$(foreach Y,$(DS),$(eval $(call concrule,$(Y),,)))
$(foreach Y,$(DSbulk),$(eval $(call concrule,$(Y),,)))
$(foreach F,$(FILT),$(foreach Y,$(DS),$(eval $(call concrule,$(Y),$(F),_$(F)))))
$(foreach F,$(FILT),$(foreach Y,$(DSbulk),$(eval $(call concrule,$(Y),$(F),_$(F)))))

## ------------------------ Calculate relative performances --------------------------- ##
## ------------------------------------------------------------------------------------ ##
define relperfrule
$(relperfdir)/$(1)$(3)_relative_performance.rds: scripts/calculate_relative_performance_all_truths.R $(cobradir)/$(1)$(3)_cobra.rds
	mkdir -p $(relperfdir)
	$(R) "--args dataset='$(1)' filt='$(2)' cobradir='$(cobradir)' outdir='$(relperfdir)'" scripts/calculate_relative_performance_all_truths.R Rout/calculate_relative_performance_all_truths_$(1)$(3).Rout
endef
$(foreach Y,$(DS),$(eval $(call relperfrule,$(Y),,)))
$(foreach Y,$(DSbulk),$(eval $(call relperfrule,$(Y),,)))
$(foreach F,$(FILT),$(foreach Y,$(DS),$(eval $(call relperfrule,$(Y),$(F),_$(F)))))
$(foreach F,$(FILT),$(foreach Y,$(DSbulk),$(eval $(call relperfrule,$(Y),$(F),_$(F)))))

## -------------------------- Calculate true performances ----------------------------- ##
## ------------------------------------------------------------------------------------ ##
define trueperfrule
$(realperfdir)/$(1)$(3)_performance.rds: scripts/calculate_performance_realtruth.R $(cobradir)/$(1)$(3)_cobra.rds data/$(1)_truth.rds
	mkdir -p $(realperfdir)
	$(R) "--args dataset='$(1)' filt='$(2)' cobradir='$(cobradir)' outdir='$(realperfdir)'" scripts/calculate_performance_realtruth.R Rout/calculate_performance_realtruth_$(1)$(3).Rout
endef
$(foreach Y,$(DSsimsignal),$(eval $(call trueperfrule,$(Y),,)))
$(foreach F,$(FILT),$(foreach Y,$(DSsimsignal),$(eval $(call trueperfrule,$(Y),$(F),_$(F)))))
#$(foreach Y,$(DSsimsignalscimpute),$(eval $(call trueperfrule,$(Y),,)))
#$(foreach F,$(FILT),$(foreach Y,$(DSsimsignalscimpute),$(eval $(call trueperfrule,$(Y),$(F),_$(F)))))
#$(foreach Y,$(DSsimsignaldrimpute),$(eval $(call trueperfrule,$(Y),,)))
#$(foreach F,$(FILT),$(foreach Y,$(DSsimsignaldrimpute),$(eval $(call trueperfrule,$(Y),$(F),_$(F)))))
#$(foreach Y,$(DSsimsignalknnsmooth),$(eval $(call trueperfrule,$(Y),,)))
#$(foreach F,$(FILT),$(foreach Y,$(DSsimsignalknnsmooth),$(eval $(call trueperfrule,$(Y),$(F),_$(F)))))

## --------------------------- Plots for evaluation ----------------------------------- ##
## ------------------------------------------------------------------------------------ ##
define plotrule
$(singledsfigdir)/$(2)/$(1)$(4)_$(2)_summary_data.rds: scripts/run_plot_single_dataset_evaluation.R scripts/plot_single_dataset_$(2).R $(cobradir)/$(1)$(4)_cobra.rds
	mkdir -p $$(@D)
	$(R) "--args dataset='$(1)' filt='$(3)' plottype='$(2)' cobradir='$(cobradir)' concordancedir='$(concordancedir)' relperfdir='$(relperfdir)' realperfdir='$(realperfdir)' figdir='$(singledsfigdir)'" scripts/run_plot_single_dataset_evaluation.R Rout/run_plot_single_dataset_evaluation_$(1)$(4)_$(2).Rout
endef
$(foreach Y,$(DS),$(foreach P,$(PLOTTYPE1),$(eval $(call plotrule,$(Y),$(P),,))))
$(foreach Y,$(DSbulk),$(foreach P,$(PLOTTYPE1),$(eval $(call plotrule,$(Y),$(P),,))))
$(foreach F,$(FILT),$(foreach Y,$(DS),$(foreach P,$(PLOTTYPE1),$(eval $(call plotrule,$(Y),$(P),$(F),_$(F))))))
$(foreach F,$(FILT),$(foreach Y,$(DSbulk),$(foreach P,$(PLOTTYPE1),$(eval $(call plotrule,$(Y),$(P),$(F),_$(F))))))

define plotrule2
$(singledsfigdir)/$(2)/$(1)$(4)_$(2)_summary_data.rds: scripts/run_plot_single_dataset_evaluation.R scripts/plot_single_dataset_$(2).R $(cobradir)/$(1)$(4)_cobra.rds \
$(concordancedir)/$(1)$(4)_concordances.rds 
	mkdir -p $$(@D)
	$(R) "--args dataset='$(1)' filt='$(3)' plottype='$(2)' cobradir='$(cobradir)' concordancedir='$(concordancedir)' relperfdir='$(relperfdir)' realperfdir='$(realperfdir)' figdir='$(singledsfigdir)'" scripts/run_plot_single_dataset_evaluation.R Rout/run_plot_single_dataset_evaluation_$(1)$(4)_$(2).Rout
endef
$(foreach Y,$(DS),$(foreach P,$(PLOTTYPE2),$(eval $(call plotrule2,$(Y),$(P),,))))
$(foreach Y,$(DSbulk),$(foreach P,$(PLOTTYPE2),$(eval $(call plotrule2,$(Y),$(P),,))))
$(foreach F,$(FILT),$(foreach Y,$(DS),$(foreach P,$(PLOTTYPE2),$(eval $(call plotrule2,$(Y),$(P),$(F),_$(F))))))
$(foreach F,$(FILT),$(foreach Y,$(DSbulk),$(foreach P,$(PLOTTYPE2),$(eval $(call plotrule2,$(Y),$(P),$(F),_$(F))))))

define plotrule3
$(singledsfigdir)/$(2)/$(1)$(4)_$(2)_summary_data.rds: scripts/run_plot_single_dataset_evaluation.R scripts/plot_single_dataset_$(2).R \
$(relperfdir)/$(1)$(4)_relative_performance.rds
	mkdir -p $$(@D)
	$(R) "--args dataset='$(1)' filt='$(3)' plottype='$(2)' cobradir='$(cobradir)' concordancedir='$(concordancedir)' relperfdir='$(relperfdir)' realperfdir='$(realperfdir)' figdir='$(singledsfigdir)'" scripts/run_plot_single_dataset_evaluation.R Rout/run_plot_single_dataset_evaluation_$(1)$(4)_$(2).Rout
endef
$(foreach Y,$(DS),$(foreach P,$(PLOTTYPE3),$(eval $(call plotrule3,$(Y),$(P),,))))
$(foreach Y,$(DSbulk),$(foreach P,$(PLOTTYPE3),$(eval $(call plotrule3,$(Y),$(P),,))))
$(foreach F,$(FILT),$(foreach Y,$(DS),$(foreach P,$(PLOTTYPE3),$(eval $(call plotrule3,$(Y),$(P),$(F),_$(F))))))
$(foreach F,$(FILT),$(foreach Y,$(DSbulk),$(foreach P,$(PLOTTYPE3),$(eval $(call plotrule3,$(Y),$(P),$(F),_$(F))))))

define plotrule4
$(singledsfigdir)/$(2)/$(1)$(4)_$(2)_summary_data.rds: scripts/run_plot_single_dataset_evaluation.R scripts/plot_single_dataset_$(2).R \
$(realperfdir)/$(1)$(4)_performance.rds
	mkdir -p $$(@D)
	$(R) "--args dataset='$(1)' filt='$(3)' plottype='$(2)' cobradir='$(cobradir)' concordancedir='$(concordancedir)' relperfdir='$(relperfdir)' realperfdir='$(realperfdir)' figdir='$(singledsfigdir)'" scripts/run_plot_single_dataset_evaluation.R Rout/run_plot_single_dataset_evaluation_$(1)$(4)_$(2).Rout
endef
$(foreach Y,$(DSsimsignal),$(foreach P,$(PLOTTYPE4),$(eval $(call plotrule4,$(Y),$(P),,))))
$(foreach F,$(FILT),$(foreach Y,$(DSsimsignal),$(foreach P,$(PLOTTYPE4),$(eval $(call plotrule4,$(Y),$(P),$(F),_$(F))))))
#$(foreach Y,$(DSsimsignalscimpute),$(foreach P,$(PLOTTYPE4),$(eval $(call plotrule4,$(Y),$(P),,))))
#$(foreach F,$(FILT),$(foreach Y,$(DSsimsignalscimpute),$(foreach P,$(PLOTTYPE4),$(eval $(call plotrule4,$(Y),$(P),$(F),_$(F))))))
#$(foreach Y,$(DSsimsignaldrimpute),$(foreach P,$(PLOTTYPE4),$(eval $(call plotrule4,$(Y),$(P),,))))
#$(foreach F,$(FILT),$(foreach Y,$(DSsimsignaldrimpute),$(foreach P,$(PLOTTYPE4),$(eval $(call plotrule4,$(Y),$(P),$(F),_$(F))))))
#$(foreach Y,$(DSsimsignalknnsmooth),$(foreach P,$(PLOTTYPE4),$(eval $(call plotrule4,$(Y),$(P),,))))
#$(foreach F,$(FILT),$(foreach Y,$(DSsimsignalknnsmooth),$(foreach P,$(PLOTTYPE4),$(eval $(call plotrule4,$(Y),$(P),$(F),_$(F))))))

## -------------------- Plots for characterization of data set ------------------------ ##
## ------------------------------------------------------------------------------------ ##
## Distributions
define plotrule_distr
$(distrdir)/$(1)$(3)_distribution_fit_summary_data.rds: scripts/run_distribution_fit.R \
data/$(1).rds subsets/$(1)_subsets.rds config/$(1).json
	mkdir -p $(distrdir)
	$(R) "--args dataset='$(1)' config_file='config/$(1).json' filt='$(2)' figdir='$(distrdir)'" scripts/run_distribution_fit.R Rout/run_distribution_fit_$(1)$(3).Rout
endef
$(foreach Y,$(DSrealmock),$(eval $(call plotrule_distr,$(Y),,)))
$(foreach Y,$(DSsimmock),$(eval $(call plotrule_distr,$(Y),,)))
$(foreach Y,$(DSbulkmock),$(eval $(call plotrule_distr,$(Y),,)))
#$(foreach Y,$(DSrealmockscimpute),$(eval $(call plotrule_distr,$(Y),,)))
#$(foreach Y,$(DSrealmockdrimpute),$(eval $(call plotrule_distr,$(Y),,)))
#$(foreach Y,$(DSrealmockknnsmooth),$(eval $(call plotrule_distr,$(Y),,)))
$(foreach F,$(FILT), $(foreach Y,$(DSrealmock),$(eval $(call plotrule_distr,$(Y),$(F),_$(F)))))
$(foreach F,$(FILT), $(foreach Y,$(DSsimmock),$(eval $(call plotrule_distr,$(Y),$(F),_$(F)))))
$(foreach F,$(FILT), $(foreach Y,$(DSbulkmock),$(eval $(call plotrule_distr,$(Y),$(F),_$(F)))))
#$(foreach F,$(FILT), $(foreach Y,$(DSrealmockscimpute),$(eval $(call plotrule_distr,$(Y),$(F),_$(F)))))
#$(foreach F,$(FILT), $(foreach Y,$(DSrealmockdrimpute),$(eval $(call plotrule_distr,$(Y),$(F),_$(F)))))
#$(foreach F,$(FILT), $(foreach Y,$(DSrealmockknnsmooth),$(eval $(call plotrule_distr,$(Y),$(F),_$(F)))))

define plotrule_characterization
$(dschardir)/$(1)$(3)_dataset_characteristics_summary_data.rds: scripts/run_plot_dataset_characterization.R \
subsets/$(1)_subsets.rds data/$(1).rds data/cell_cycle_geneids.rds
	mkdir -p $(dschardir)
	$(R) "--args dataset='$(1)' config_file='config/$(1).json' filt='$(2)' cell_cycle_file='data/cell_cycle_geneids.rds' figdir='$(dschardir)'" scripts/run_plot_dataset_characterization.R Rout/run_plot_dataset_characterization_$(1)$(3).Rout
endef
$(foreach Y,$(DSnonimpute),$(eval $(call plotrule_characterization,$(Y),,)))
$(foreach Y,$(DSbulk),$(eval $(call plotrule_characterization,$(Y),,)))
$(foreach F,$(FILT), $(foreach Y,$(DSnonimpute),$(eval $(call plotrule_characterization,$(Y),$(F),_$(F)))))
$(foreach F,$(FILT), $(foreach Y,$(DSbulk),$(eval $(call plotrule_characterization,$(Y),$(F),_$(F)))))

#define plotrule_characterizationscimpute
#$(dschardir)/$(1)$(3)_dataset_characteristics_summary_data.rds: scripts/run_plot_dataset_characterization.R \
#subsets/$(1)_subsets.rds data/$(1).rds scripts/scimpute_dropouts.R data/cell_cycle_geneids.rds
#	mkdir -p $(dschardir)
#	$(R) "--args dataset='$(1)' config_file='config/$(1).json' filt='$(2)' cell_cycle_file='data/cell_cycle_geneids.rds' figdir='$(dschardir)'" scripts/run_plot_dataset_characterization.R Rout/run_plot_dataset_characterization_$(1)$(3).Rout
#endef
#$(foreach Y,$(DSscimpute),$(eval $(call plotrule_characterizationscimpute,$(Y),,)))
#$(foreach F,$(FILT), $(foreach Y,$(DSscimpute),$(eval $(call plotrule_characterizationscimpute,$(Y),$(F),_$(F)))))

#define plotrule_characterizationdrimpute
#$(dschardir)/$(1)$(3)_dataset_characteristics_summary_data.rds: scripts/run_plot_dataset_characterization.R \
#subsets/$(1)_subsets.rds data/$(1).rds scripts/drimpute_dropouts.R data/cell_cycle_geneids.rds
#	mkdir -p $(dschardir)
#	$(R) "--args dataset='$(1)' config_file='config/$(1).json' filt='$(2)' cell_cycle_file='data/cell_cycle_geneids.rds' figdir='$(dschardir)'" scripts/run_plot_dataset_characterization.R Rout/run_plot_dataset_characterization_$(1)$(3).Rout
#endef
#$(foreach Y,$(DSdrimpute),$(eval $(call plotrule_characterizationdrimpute,$(Y),,)))
#$(foreach F,$(FILT), $(foreach Y,$(DSdrimpute),$(eval $(call plotrule_characterizationdrimpute,$(Y),$(F),_$(F)))))

#define plotrule_characterizationknnsmooth
#$(dschardir)/$(1)$(3)_dataset_characteristics_summary_data.rds: scripts/run_plot_dataset_characterization.R \
#subsets/$(1)_subsets.rds data/$(1).rds scripts/knnsmooth_dropouts.R data/cell_cycle_geneids.rds
#	mkdir -p $(dschardir)
#	$(R) "--args dataset='$(1)' config_file='config/$(1).json' filt='$(2)' cell_cycle_file='data/cell_cycle_geneids.rds' figdir='$(dschardir)'" scripts/run_plot_dataset_characterization.R Rout/run_plot_dataset_characterization_$(1)$(3).Rout
#endef
#$(foreach Y,$(DSknnsmooth),$(eval $(call plotrule_characterizationknnsmooth,$(Y),,)))
#$(foreach F,$(FILT), $(foreach Y,$(DSknnsmooth),$(eval $(call plotrule_characterizationknnsmooth,$(Y),$(F),_$(F)))))

## -------------------- Plots for evaluation, orig vs mock ---------------------------- ##
## ------------------------------------------------------------------------------------ ##
define origvsmockrule
$(figdir)/orig_vs_mock/$(1)$(3)_orig_vs_mock_summary_data.rds: $(concordancedir)/$(1)$(3)_concordances.rds \
$(concordancedir)/$(1)mock$(3)_concordances.rds \
scripts/run_plot_single_dataset_origvsmock.R 
	mkdir -p $$(@D)
	$(R) "--args dataset='$(1)' filt='$(2)' concordancedir='$(concordancedir)' figdir='$(figdir)/orig_vs_mock'" scripts/run_plot_single_dataset_origvsmock.R Rout/run_plot_single_dataset_origvsmock_$(1)$(3).Rout
endef
$(foreach Y,$(Dsb),$(eval $(call origvsmockrule,$(Y),,)))
$(foreach Y,$(DSbulksignal),$(eval $(call origvsmockrule,$(Y),,)))
$(foreach Y,$(Dsbsim),$(eval $(call origvsmockrule,$(Y),,)))
$(foreach F,$(FILT), $(foreach Y,$(Dsb),$(eval $(call origvsmockrule,$(Y),$(F),_$(F)))))
$(foreach F,$(FILT), $(foreach Y,$(DSbulksignal),$(eval $(call origvsmockrule,$(Y),$(F),_$(F)))))
$(foreach F,$(FILT), $(foreach Y,$(Dsbsim),$(eval $(call origvsmockrule,$(Y),$(F),_$(F)))))
#$(foreach Y,$(Dsbscimpute),$(eval $(call origvsmockrule,$(Y),,)))
#$(foreach Y,$(Dsbsimscimpute),$(eval $(call origvsmockrule,$(Y),,)))
#$(foreach F,$(FILT), $(foreach Y,$(Dsbscimpute),$(eval $(call origvsmockrule,$(Y),$(F),_$(F)))))
#$(foreach F,$(FILT), $(foreach Y,$(Dsbsimscimpute),$(eval $(call origvsmockrule,$(Y),$(F),_$(F)))))
#$(foreach Y,$(Dsbdrimpute),$(eval $(call origvsmockrule,$(Y),,)))
#$(foreach Y,$(Dsbsimdrimpute),$(eval $(call origvsmockrule,$(Y),,)))
#$(foreach F,$(FILT), $(foreach Y,$(Dsbdrimpute),$(eval $(call origvsmockrule,$(Y),$(F),_$(F)))))
#$(foreach F,$(FILT), $(foreach Y,$(Dsbsimdrimpute),$(eval $(call origvsmockrule,$(Y),$(F),_$(F)))))
#$(foreach Y,$(Dsbknnsmooth),$(eval $(call origvsmockrule,$(Y),,)))
#$(foreach Y,$(Dsbsimknnsmooth),$(eval $(call origvsmockrule,$(Y),,)))
#$(foreach F,$(FILT), $(foreach Y,$(Dsbknnsmooth),$(eval $(call origvsmockrule,$(Y),$(F),_$(F)))))
#$(foreach F,$(FILT), $(foreach Y,$(Dsbsimknnsmooth),$(eval $(call origvsmockrule,$(Y),$(F),_$(F)))))

## ------------------------ Summary plots, across data sets --------------------------- ##
## ------------------------------------------------------------------------------------ ##
define summaryrule_timing
$(multidsfigdir)/timing/summary_timing$(1).rds: $(addsuffix _summary_data.rds, $(addprefix $(singledsfigdir)/timing/, $(foreach Y,$(2),$(Y)_timing))) \
$(addsuffix _summary_data.rds, $(addprefix $(singledsfigdir)/timing/, $(foreach F,$(4),$(foreach Y,$(2),$(Y)_$(F)_timing)))) \
scripts/run_plot_multi_dataset_summarization.R scripts/summarize_timing.R include_datasets.mk include_filterings.mk plot_methods.mk
	mkdir -p $$(@D)
	$(R) "--args datasets='$(3)' filt='$(5)' summarytype='timing' dstypetxt='$(dstypetxt)' plotmethods='$(6)' dtpext='$(1)' figdir='$(multidsfigdir)/timing' singledsfigdir='$(singledsfigdir)' cobradir='$(cobradir)' dschardir='$(dschardir)' origvsmockdir='$(figdir)/orig_vs_mock' distrdir='$(distrdir)' concordancedir='$(concordancedir)'" scripts/run_plot_multi_dataset_summarization.R Rout/run_plot_multi_dataset_summarization_timing$(1).Rout
endef
$(eval $(call summaryrule_timing,_all,$(DSnonimpute),${DSnonimputec},$(FILT),${FILTc},${MTplotc}))

define summaryrule_runfailure
$(multidsfigdir)/runfailure/summary_runfailure$(1).rds: $(addsuffix _summary_data.rds, $(addprefix $(singledsfigdir)/runfailure/, $(foreach Y,$(2),$(Y)_runfailure))) \
$(addsuffix _summary_data.rds, $(addprefix $(singledsfigdir)/runfailure/, $(foreach F,$(4),$(foreach Y,$(2),$(Y)_$(F)_runfailure)))) \
scripts/run_plot_multi_dataset_summarization.R scripts/summarize_runfailure.R include_datasets.mk include_filterings.mk plot_methods.mk
	mkdir -p $$(@D)
	$(R) "--args datasets='$(3)' filt='$(5)' summarytype='runfailure' dstypetxt='$(dstypetxt)' plotmethods='$(6)' dtpext='$(1)' figdir='$(multidsfigdir)/runfailure' singledsfigdir='$(singledsfigdir)' cobradir='$(cobradir)' dschardir='$(dschardir)' origvsmockdir='$(figdir)/orig_vs_mock' distrdir='$(distrdir)' concordancedir='$(concordancedir)'" scripts/run_plot_multi_dataset_summarization.R Rout/run_plot_multi_dataset_summarization_runfailure$(1).Rout
endef
$(eval $(call summaryrule_runfailure,_all,$(DSnonimpute),${DSnonimputec},$(FILT),${FILTc},${MTplotc}))

define summaryrule_fracNA
$(multidsfigdir)/fracNA/summary_fracNA$(1).rds: $(addsuffix _cobra.rds, $(addprefix $(cobradir)/, $(foreach Y,$(2),$(Y)))) \
$(addsuffix _cobra.rds, $(addprefix $(cobradir)/, $(foreach F,$(4),$(foreach Y,$(2),$(Y)_$(F))))) \
scripts/run_plot_multi_dataset_summarization.R scripts/summarize_fracNA.R include_datasets.mk include_filterings.mk plot_methods.mk
	mkdir -p $$(@D)
	$(R) "--args datasets='$(3)' filt='$(5)' summarytype='fracNA' dstypetxt='$(dstypetxt)' plotmethods='$(6)' dtpext='$(1)' figdir='$(multidsfigdir)/fracNA' singledsfigdir='$(singledsfigdir)' cobradir='$(cobradir)' dschardir='$(dschardir)' origvsmockdir='$(figdir)/orig_vs_mock' distrdir='$(distrdir)' concordancedir='$(concordancedir)'" scripts/run_plot_multi_dataset_summarization.R Rout/run_plot_multi_dataset_summarization_fracNA$(1).Rout
endef
$(eval $(call summaryrule_fracNA,_real,$(DSreal),${DSrealc},$(FILT),${FILTc},${MTplotc}))
$(eval $(call summaryrule_fracNA,_bulk,$(DSbulk),${DSbulkc},$(FILT),${FILTc},${MTplotc}))
#$(eval $(call summaryrule_fracNA,_realscimpute,$(DSrealscimpute),${DSrealscimputec},$(FILT),${FILTc},${MTplotc}))
#$(eval $(call summaryrule_fracNA,_realdrimpute,$(DSrealdrimpute),${DSrealdrimputec},$(FILT),${FILTc},${MTplotc}))
#$(eval $(call summaryrule_fracNA,_realknnsmooth,$(DSrealknnsmooth),${DSrealknnsmoothc},$(FILT),${FILTc},${MTplotc}))

define summaryrule_nbrdet
$(multidsfigdir)/nbrdet/summary_nbrdet$(1).rds: $(addsuffix _cobra.rds, $(addprefix $(cobradir)/, $(foreach Y,$(2),$(Y)))) \
$(addsuffix _cobra.rds, $(addprefix $(cobradir)/, $(foreach F,$(4),$(foreach Y,$(2),$(Y)_$(F))))) \
scripts/run_plot_multi_dataset_summarization.R scripts/summarize_nbrdet.R include_datasets.mk include_filterings.mk plot_methods.mk
	mkdir -p $$(@D)
	$(R) "--args datasets='$(3)' filt='$(5)' summarytype='nbrdet' dstypetxt='$(dstypetxt)' plotmethods='$(6)' dtpext='$(1)' figdir='$(multidsfigdir)/nbrdet' singledsfigdir='$(singledsfigdir)' cobradir='$(cobradir)' dschardir='$(dschardir)' origvsmockdir='$(figdir)/orig_vs_mock' distrdir='$(distrdir)' concordancedir='$(concordancedir)'" scripts/run_plot_multi_dataset_summarization.R Rout/run_plot_multi_dataset_summarization_nbrdet$(1).Rout
endef
$(eval $(call summaryrule_nbrdet,_real,$(DSrealsignal),${DSrealsignalc},$(FILT),${FILTc},${MTplotc}))
$(eval $(call summaryrule_nbrdet,_bulk,$(DSbulksignal),${DSbulksignalc},$(FILT),${FILTc},${MTplotc}))
#$(eval $(call summaryrule_nbrdet,_realscimpute,$(DSrealsignalscimpute),${DSrealsignalscimputec},$(FILT),${FILTc},${MTplotc}))
#$(eval $(call summaryrule_nbrdet,_realdrimpute,$(DSrealsignaldrimpute),${DSrealsignaldrimputec},$(FILT),${FILTc},${MTplotc}))
#$(eval $(call summaryrule_nbrdet,_realknnsmooth,$(DSrealsignalknnsmooth),${DSrealsignalknnsmoothc},$(FILT),${FILTc},${MTplotc}))

define summaryrule_truefpr
$(multidsfigdir)/truefpr/summary_truefpr$(1).rds: $(addsuffix _summary_data.rds, $(addprefix $(singledsfigdir)/truefpr/, $(foreach Y,$(2),$(Y)_truefpr))) \
$(addsuffix _summary_data.rds, $(addprefix $(singledsfigdir)/truefpr/, $(foreach F,$(4),$(foreach Y,$(2),$(Y)_$(F)_truefpr)))) \
scripts/run_plot_multi_dataset_summarization.R scripts/summarize_truefpr.R include_datasets.mk include_filterings.mk plot_methods.mk
	mkdir -p $$(@D)
	$(R) "--args datasets='$(3)' filt='$(5)' summarytype='truefpr' dstypetxt='$(dstypetxt)' plotmethods='$(6)' dtpext='$(1)' figdir='$(multidsfigdir)/truefpr' singledsfigdir='$(singledsfigdir)' cobradir='$(cobradir)' dschardir='$(dschardir)' origvsmockdir='$(figdir)/orig_vs_mock' distrdir='$(distrdir)' concordancedir='$(concordancedir)'" scripts/run_plot_multi_dataset_summarization.R Rout/run_plot_multi_dataset_summarization_truefpr$(1).Rout
endef
$(eval $(call summaryrule_truefpr,_real,$(DSrealmock),${DSrealmockc},$(FILT),${FILTc},${MTplotc}))
$(eval $(call summaryrule_truefpr,_sim,$(DSsimmock),${DSsimmockc},$(FILT),${FILTc},${MTplotc}))
$(eval $(call summaryrule_truefpr,_bulk,$(DSbulkmock),${DSbulkmockc},$(FILT),${FILTc},${MTplotc}))
#$(eval $(call summaryrule_truefpr,_realscimpute,$(DSrealmockscimpute),${DSrealmockscimputec},$(FILT),${FILTc},${MTplotc}))
#$(eval $(call summaryrule_truefpr,_simscimpute,$(DSsimmockscimpute),${DSsimmockscimputec},$(FILT),${FILTc},${MTplotc}))
#$(eval $(call summaryrule_truefpr,_realdrimpute,$(DSrealmockdrimpute),${DSrealmockdrimputec},$(FILT),${FILTc},${MTplotc}))
#$(eval $(call summaryrule_truefpr,_simdrimpute,$(DSsimmockdrimpute),${DSsimmockdrimputec},$(FILT),${FILTc},${MTplotc}))
#$(eval $(call summaryrule_truefpr,_realknnsmooth,$(DSrealmockknnsmooth),${DSrealmockknnsmoothc},$(FILT),${FILTc},${MTplotc}))
#$(eval $(call summaryrule_truefpr,_simknnsmooth,$(DSsimmockknnsmooth),${DSsimmockknnsmoothc},$(FILT),${FILTc},${MTplotc}))

define summaryrule_pvalhist
$(multidsfigdir)/pvalhist/summary_pvalhist$(1).rds: $(addsuffix _cobra.rds, $(addprefix $(cobradir)/, $(foreach Y,$(2),$(Y)))) \
$(addsuffix _cobra.rds, $(addprefix $(cobradir)/, $(foreach F,$(4),$(foreach Y,$(2),$(Y)_$(F))))) \
scripts/run_plot_multi_dataset_summarization.R scripts/summarize_pvalhist.R include_datasets.mk include_filterings.mk plot_methods.mk
	mkdir -p $$(@D)
	$(R) "--args datasets='$(3)' filt='$(5)' summarytype='pvalhist' dstypetxt='$(dstypetxt)' plotmethods='$(6)' dtpext='$(1)' figdir='$(multidsfigdir)/pvalhist' singledsfigdir='$(singledsfigdir)' cobradir='$(cobradir)' dschardir='$(dschardir)' origvsmockdir='$(figdir)/orig_vs_mock' distrdir='$(distrdir)' concordancedir='$(concordancedir)'" scripts/run_plot_multi_dataset_summarization.R Rout/run_plot_multi_dataset_summarization_pvalhist$(1).Rout
endef
$(eval $(call summaryrule_pvalhist,_real,$(DSrealmock),${DSrealmockc},$(FILT),${FILTc},${MTplotc}))

define summaryrule_de_characteristics
$(multidsfigdir)/de_characteristics/summary_de_characteristics$(1).rds: $(addsuffix _summary_data.rds, $(addprefix $(singledsfigdir)/results_characterization/, $(foreach Y,$(2),$(Y)_results_characterization))) \
scripts/run_plot_multi_dataset_summarization.R scripts/summarize_de_characteristics.R include_datasets.mk include_filterings.mk plot_methods.mk
	mkdir -p $$(@D)
	$(R) "--args datasets='$(3)' filt='$(5)' summarytype='de_characteristics' dstypetxt='$(dstypetxt)' plotmethods='$(6)' dtpext='$(1)' figdir='$(multidsfigdir)/de_characteristics' singledsfigdir='$(singledsfigdir)' cobradir='$(cobradir)' dschardir='$(dschardir)' origvsmockdir='$(figdir)/orig_vs_mock' distrdir='$(distrdir)' concordancedir='$(concordancedir)'" scripts/run_plot_multi_dataset_summarization.R Rout/run_plot_multi_dataset_summarization_de_characteristics$(1).Rout
endef
$(eval $(call summaryrule_de_characteristics,_real,$(DSrealmock),${DSrealmockc},,,${MTplotc}))
$(eval $(call summaryrule_de_characteristics,_sim,$(DSsimmock),${DSsimmockc},,,${MTplotc}))
#$(eval $(call summaryrule_de_characteristics,_realscimpute,$(DSrealmockscimpute),${DSrealmockscimputec},,,${MTplotc}))
#$(eval $(call summaryrule_de_characteristics,_simscimpute,$(DSsimmockscimpute),${DSsimmockscimputec},,,${MTplotc}))
#$(eval $(call summaryrule_de_characteristics,_realdrimpute,$(DSrealmockdrimpute),${DSrealmockdrimputec},,,${MTplotc}))
#$(eval $(call summaryrule_de_characteristics,_simdrimpute,$(DSsimmockdrimpute),${DSsimmockdrimputec},,,${MTplotc}))
#$(eval $(call summaryrule_de_characteristics,_realknnsmooth,$(DSrealmockknnsmooth),${DSrealmockknnsmoothc},,,${MTplotc}))
#$(eval $(call summaryrule_de_characteristics,_simknnsmooth,$(DSsimmockknnsmooth),${DSsimmockknnsmoothc},,,${MTplotc}))

define summaryrule_crossmethod_consistency
$(multidsfigdir)/crossmethod_consistency/summary_crossmethod_consistency$(1).rds: \
$(addsuffix .rds, $(addprefix $(concordancedir)/, $(foreach Y,$(2),$(Y)_concordances))) \
$(addsuffix .rds, $(addprefix $(concordancedir)/, $(foreach F,$(4),$(foreach Y,$(2),$(Y)_$(F)_concordances)))) \
$(addsuffix .rds, $(addprefix $(dschardir)/, $(foreach Y,$(2),$(Y)_dataset_characteristics_summary_data))) \
$(addsuffix .rds, $(addprefix $(dschardir)/, $(foreach F,$(4),$(foreach Y,$(2),$(Y)_$(F)_dataset_characteristics_summary_data)))) \
scripts/run_plot_multi_dataset_summarization.R scripts/summarize_crossmethod_consistency.R \
include_datasets.mk include_filterings.mk plot_methods.mk
	mkdir -p $$(@D)
	$(R) "--args datasets='$(3)' filt='$(5)' summarytype='crossmethod_consistency' dstypetxt='$(dstypetxt)' plotmethods='$(6)' dtpext='$(1)' figdir='$(multidsfigdir)/crossmethod_consistency' singledsfigdir='$(singledsfigdir)' cobradir='$(cobradir)' dschardir='$(dschardir)' origvsmockdir='$(figdir)/orig_vs_mock' distrdir='$(distrdir)' concordancedir='$(concordancedir)'" scripts/run_plot_multi_dataset_summarization.R Rout/run_plot_multi_dataset_summarization_crossmethod_consistency$(1).Rout
endef
$(eval $(call summaryrule_crossmethod_consistency,_real,$(DSrealsignal),${DSrealsignalc},$(FILT),${FILTc},${MTplotc}))
$(eval $(call summaryrule_crossmethod_consistency,_sim,$(DSsimsignal),${DSsimsignalc},$(FILT),${FILTc},${MTplotc}))
$(eval $(call summaryrule_crossmethod_consistency,_bulk,$(DSbulksignal),${DSbulksignalc},$(FILT),${FILTc},${MTplotc}))
#$(eval $(call summaryrule_crossmethod_consistency,_realscimpute,$(DSrealsignalscimpute),${DSrealsignalscimputec},$(FILT),${FILTc},${MTplotc}))
#$(eval $(call summaryrule_crossmethod_consistency,_simscimpute,$(DSsimsignalscimpute),${DSsimsignalscimputec},$(FILT),${FILTc},${MTplotc}))
#$(eval $(call summaryrule_crossmethod_consistency,_realdrimpute,$(DSrealsignaldrimpute),${DSrealsignaldrimputec},$(FILT),${FILTc},${MTplotc}))
#$(eval $(call summaryrule_crossmethod_consistency,_simdrimpute,$(DSsimsignaldrimpute),${DSsimsignaldrimputec},$(FILT),${FILTc},${MTplotc}))
#$(eval $(call summaryrule_crossmethod_consistency,_realknnsmooth,$(DSrealsignalknnsmooth),${DSrealsignalknnsmoothc},$(FILT),${FILTc},${MTplotc}))
#$(eval $(call summaryrule_crossmethod_consistency,_simknnsmooth,$(DSsimsignalknnsmooth),${DSsimsignalknnsmoothc},$(FILT),${FILTc},${MTplotc}))

define clustannotrule
$(multidsfigdir)/crossmethod_consistency/crossmethod_consistency_final$(1)_$(2)_hclust_annot.rds: \
$(multidsfigdir)/crossmethod_consistency/summary_crossmethod_consistency$(1).rds \
DEmethod_characteristics.txt scripts/annotate_method_clustering.R
	mkdir -p $$(@D)
	$(R34) "--args hclustrds='$(multidsfigdir)/crossmethod_consistency/crossmethod_consistency_final$(1)_$(2)_plots.rds' chartxt='DEmethod_characteristics.txt' outrds='$$(@)'" scripts/annotate_method_clustering.R Rout/annotate_method_clustering$(1)_$(2).Rout
endef
$(eval $(call clustannotrule,_real,100))

define summaryrule_relfprtpr
$(multidsfigdir)/relfprtpr/summary_relfprtpr$(1).rds: $(addsuffix _summary_data.rds, $(addprefix $(singledsfigdir)/results_relativetruth/, $(foreach Y,$(2),$(Y)_results_relativetruth))) \
$(addsuffix _summary_data.rds, $(addprefix $(singledsfigdir)/results_relativetruth/, $(foreach F,$(4),$(foreach Y,$(2),$(Y)_$(F)_results_relativetruth)))) \
scripts/run_plot_multi_dataset_summarization.R scripts/summarize_relfprtpr.R include_datasets.mk include_filterings.mk plot_methods.mk
	mkdir -p $$(@D)
	$(R) "--args datasets='$(3)' filt='$(5)' summarytype='relfprtpr' dstypetxt='$(dstypetxt)' plotmethods='$(6)' dtpext='$(1)' figdir='$(multidsfigdir)/relfprtpr' singledsfigdir='$(singledsfigdir)' cobradir='$(cobradir)' dschardir='$(dschardir)' origvsmockdir='$(figdir)/orig_vs_mock' distrdir='$(distrdir)' concordancedir='$(concordancedir)'" scripts/run_plot_multi_dataset_summarization.R Rout/run_plot_multi_dataset_summarization_relfprtpr$(1).Rout
endef
$(eval $(call summaryrule_relfprtpr,_real,$(DSrealsignal),${DSrealsignalc},$(FILT),${FILTc},${MTplotc}))
$(eval $(call summaryrule_relfprtpr,_sim,$(DSsimsignal),${DSsimsignalc},$(FILT),${FILTc},${MTplotc}))
#$(eval $(call summaryrule_relfprtpr,_realscimpute,$(DSrealsignalscimpute),${DSrealsignalscimputec},$(FILT),${FILTc},${MTplotc}))
#$(eval $(call summaryrule_relfprtpr,_simscimpute,$(DSsimsignalscimpute),${DSsimsignalscimputec},$(FILT),${FILTc},${MTplotc}))
#$(eval $(call summaryrule_relfprtpr,_realdrimpute,$(DSrealsignaldrimpute),${DSrealsignaldrimputec},$(FILT),${FILTc},${MTplotc}))
#$(eval $(call summaryrule_relfprtpr,_simdrimpute,$(DSsimsignaldrimpute),${DSsimsignaldrimputec},$(FILT),${FILTc},${MTplotc}))
#$(eval $(call summaryrule_relfprtpr,_realknnsmooth,$(DSrealsignalknnsmooth),${DSrealsignalknnsmoothc},$(FILT),${FILTc},${MTplotc}))
#$(eval $(call summaryrule_relfprtpr,_simknnsmooth,$(DSsimsignalknnsmooth),${DSsimsignalknnsmoothc},$(FILT),${FILTc},${MTplotc}))

define summaryrule_filtering
$(multidsfigdir)/filtering/summary_filtering_$(1)$(2).rds: $(addsuffix _cobra.rds, $(addprefix $(cobradir)/, $(foreach Y,$(3),$(Y)_$(1)))) \
$(addsuffix _cobra.rds, $(addprefix $(cobradir)/, $(foreach Y,$(3),$(Y)))) scripts/run_plot_multi_dataset_summarization.R scripts/summarize_filtering.R \
include_datasets.mk include_filterings.mk $(addsuffix _dataset_characteristics_summary_data.rds, $(addprefix $(dschardir)/, $(foreach Y,$(3),$(Y))))
	mkdir -p $$(@D)
	$(R) "--args datasets='$(4)' filt='$(1)' summarytype='filtering' dstypetxt='$(dstypetxt)' plotmethods='$(5)' dtpext='$(2)' figdir='$(multidsfigdir)/filtering' singledsfigdir='$(singledsfigdir)' cobradir='$(cobradir)' dschardir='$(dschardir)' origvsmockdir='$(figdir)/orig_vs_mock' distrdir='$(distrdir)' concordancedir='$(concordancedir)'" scripts/run_plot_multi_dataset_summarization.R Rout/run_plot_multi_dataset_summarization_filtering_$(1)$(2).Rout
endef
$(foreach F,$(FILT),$(eval $(call summaryrule_filtering,$(F),_real,$(DSrealsignal),${DSrealsignalc},)))
$(foreach F,$(FILT),$(eval $(call summaryrule_filtering,$(F),_sim,$(DSsimsignal),${DSsimsignalc},)))
$(foreach F,$(FILT),$(eval $(call summaryrule_filtering,$(F),_bulk,$(DSbulksignal),${DSbulksignal},)))
#$(foreach F,$(FILT),$(eval $(call summaryrule_filtering,$(F),_realscimpute,$(DSrealsignalscimpute),${DSrealsignalscimputec},)))
#$(foreach F,$(FILT),$(eval $(call summaryrule_filtering,$(F),_simscimpute,$(DSsimsignalscimpute),${DSsimsignalscimputec},)))
#$(foreach F,$(FILT),$(eval $(call summaryrule_filtering,$(F),_realdrimpute,$(DSrealsignaldrimpute),${DSrealsignaldrimputec},)))
#$(foreach F,$(FILT),$(eval $(call summaryrule_filtering,$(F),_simdrimpute,$(DSsimsignaldrimpute),${DSsimsignaldrimputec},)))
#$(foreach F,$(FILT),$(eval $(call summaryrule_filtering,$(F),_realknnsmooth,$(DSrealsignalknnsmooth),${DSrealsignalknnsmoothc},)))
#$(foreach F,$(FILT),$(eval $(call summaryrule_filtering,$(F),_simknnsmooth,$(DSsimsignalknnsmooth),${DSsimsignalknnsmoothc},)))

define summaryrule_trueperformance
$(multidsfigdir)/trueperformance/summary_trueperformance$(1).rds: $(addsuffix _summary_data.rds, $(addprefix $(singledsfigdir)/performance_realtruth/, $(foreach Y,$(2),$(Y)_performance_realtruth))) \
$(addsuffix _summary_data.rds, $(addprefix $(singledsfigdir)/performance_realtruth/, $(foreach F,$(4),$(foreach Y,$(2),$(Y)_$(F)_performance_realtruth)))) \
scripts/run_plot_multi_dataset_summarization.R scripts/summarize_trueperformance.R include_datasets.mk include_filterings.mk plot_methods.mk
	mkdir -p $$(@D)
	$(R) "--args datasets='$(3)' filt='$(5)' summarytype='trueperformance' dstypetxt='$(dstypetxt)' plotmethods='$(6)' dtpext='$(1)' figdir='$(multidsfigdir)/trueperformance' singledsfigdir='$(singledsfigdir)' cobradir='$(cobradir)' dschardir='$(dschardir)' origvsmockdir='$(figdir)/orig_vs_mock' distrdir='$(distrdir)' concordancedir='$(concordancedir)'" scripts/run_plot_multi_dataset_summarization.R Rout/run_plot_multi_dataset_summarization_trueperformance$(1).Rout
endef
$(eval $(call summaryrule_trueperformance,_sim,$(DSsimsignal),${DSsimsignalc},$(FILT),${FILTc},${MTplotc}))
#$(eval $(call summaryrule_trueperformance,_simscimpute,$(DSsimsignalscimpute),${DSsimsignalscimputec},$(FILT),${FILTc},${MTplotc}))
#$(eval $(call summaryrule_trueperformance,_simdrimpute,$(DSsimsignaldrimpute),${DSsimsignaldrimputec},$(FILT),${FILTc},${MTplotc}))
#$(eval $(call summaryrule_trueperformance,_simknnsmooth,$(DSsimsignalknnsmooth),${DSsimsignalknnsmoothc},$(FILT),${FILTc},${MTplotc}))

define summaryrule_origvsmock
$(multidsfigdir)/orig_vs_mock/summary_orig_vs_mock$(1).rds: $(addsuffix _orig_vs_mock_summary_data.rds, $(addprefix $(figdir)/orig_vs_mock/, $(foreach Y,$(2),$(Y)))) \
$(addsuffix _orig_vs_mock_summary_data.rds, $(addprefix $(figdir)/orig_vs_mock/, $(foreach F,$(4),$(foreach Y,$(2),$(Y)_$(F))))) \
scripts/run_plot_multi_dataset_summarization.R scripts/summarize_orig_vs_mock.R include_datasets.mk include_filterings.mk plot_methods.mk
	mkdir -p $$(@D)
	$(R) "--args datasets='$(3)' filt='$(5)' summarytype='orig_vs_mock' dstypetxt='$(dstypetxt)' plotmethods='$(6)' dtpext='$(1)' figdir='$(multidsfigdir)/orig_vs_mock' singledsfigdir='$(singledsfigdir)' cobradir='$(cobradir)' dschardir='$(dschardir)' origvsmockdir='$(figdir)/orig_vs_mock' distrdir='$(distrdir)' concordancedir='$(concordancedir)'" scripts/run_plot_multi_dataset_summarization.R Rout/run_plot_multi_dataset_summarization_orig_vs_mock$(1).Rout
endef
$(eval $(call summaryrule_origvsmock,_real,$(Dsb),${Dsbc},$(FILT),${FILTc},${MTplotc}))
$(eval $(call summaryrule_origvsmock,_sim,$(Dsbsim),${Dsbsimc},$(FILT),${FILTc},${MTplotc}))
$(eval $(call summaryrule_origvsmock,_bulk,$(DSbulksignal),${DSbulksignalc},$(FILT),${FILTc},${MTplotc}))
#$(eval $(call summaryrule_origvsmock,_realscimpute,$(Dsbscimpute),${Dsbscimputec},$(FILT),${FILTc},${MTplotc}))
#$(eval $(call summaryrule_origvsmock,_simscimpute,$(Dsbsimscimpute),${Dsbsimscimputec},$(FILT),${FILTc},${MTplotc}))
#$(eval $(call summaryrule_origvsmock,_realdrimpute,$(Dsbdrimpute),${Dsbdrimputec},$(FILT),${FILTc},${MTplotc}))
#$(eval $(call summaryrule_origvsmock,_simdrimpute,$(Dsbsimdrimpute),${Dsbsimdrimputec},$(FILT),${FILTc},${MTplotc}))
#$(eval $(call summaryrule_origvsmock,_realknnsmooth,$(Dsbknnsmooth),${Dsbknnsmoothc},$(FILT),${FILTc},${MTplotc}))
#$(eval $(call summaryrule_origvsmock,_simknnsmooth,$(Dsbsimknnsmooth),${Dsbsimknnsmoothc},$(FILT),${FILTc},${MTplotc}))

define summaryrule_tsne
$(multidsfigdir)/tsne/summary_tsne$(1).rds: $(addsuffix _dataset_characteristics_summary_data.rds, $(addprefix $(dschardir)/, $(foreach Y,$(2),$(Y)))) \
scripts/run_plot_multi_dataset_summarization.R scripts/summarize_tsne.R include_datasets.mk
	mkdir -p $$(@D)
	$(R) "--args datasets='$(3)' filt='$(4)' summarytype='tsne' dstypetxt='$(dstypetxt)' plotmethods='$(5)' dtpext='$(1)' figdir='$(multidsfigdir)/tsne' singledsfigdir='$(singledsfigdir)' cobradir='$(cobradir)' dschardir='$(dschardir)' origvsmockdir='$(figdir)/orig_vs_mock' distrdir='$(distrdir)' concordancedir='$(concordancedir)'" scripts/run_plot_multi_dataset_summarization.R Rout/run_plot_multi_dataset_summarization_tsne$(1).Rout
endef
$(eval $(call summaryrule_tsne,_real,$(DStsne),${DStsnec},,))
$(eval $(call summaryrule_tsne,_sim,$(DSsimsignal),${DSsimsignalc},,))

define summaryrule_dschar
$(multidsfigdir)/ds_characteristics/summary_ds_characteristics$(1).rds: $(addsuffix _dataset_characteristics_summary_data.rds, $(addprefix $(dschardir)/, $(foreach Y,$(2),$(Y)))) \
scripts/run_plot_multi_dataset_summarization.R scripts/summarize_ds_characteristics.R include_datasets.mk \
$(addsuffix _distribution_fit_summary_data.rds, $(addprefix $(distrdir)/, $(foreach Y,$(6),$(Y)))) \
$(addsuffix _distribution_fit_summary_data.rds, $(addprefix $(distrdir)/, $(foreach F,$(4),$(foreach Y,$(6),$(Y)_$(F)))))
	mkdir -p $$(@D)
	$(R) "--args datasets='$(3)' filt='$(5)' summarytype='ds_characteristics' dstypetxt='$(dstypetxt)' plotmethods='$(7)' dtpext='$(1)' figdir='$(multidsfigdir)/ds_characteristics' singledsfigdir='$(singledsfigdir)' cobradir='$(cobradir)' dschardir='$(dschardir)' origvsmockdir='$(figdir)/orig_vs_mock' distrdir='$(distrdir)' concordancedir='$(concordancedir)'" scripts/run_plot_multi_dataset_summarization.R Rout/run_plot_multi_dataset_summarization_ds_characteristics$(1).Rout
endef
$(eval $(call summaryrule_dschar,_real,$(DSrealsignal),${DSrealsignalc},$(FILT),${FILTc},$(DSrealmock),))
$(eval $(call summaryrule_dschar,_sim,$(DSsimsignal),${DSsimsignalc},$(FILT),${FILTc},$(DSsimmock),))
$(eval $(call summaryrule_dschar,_bulk,$(DSbulksignal),${DSbulksignalc},$(FILT),${FILTc},$(DSbulkmock),))

## --------------------- Investigation of voom/limma behaviour ------------------------ ##
## ------------------------------------------------------------------------------------ ##
figures/misc/voomlimma_investigation.rds: $(addsuffix _subsets.rds, $(addprefix subsets/, $(foreach D,$(DSrealmock),$(D)))) \
$(addsuffix .rds, $(addprefix data/, $(foreach D,$(DSrealmock),$(D)))) scripts/investigate_voomlimma_results.R 
	mkdir -p $(@D)
	$(R) "--args figdir='figures/misc'" scripts/investigate_voomlimma_results.R Rout/investigate_voomlimma_results.Rout

## ------------------------- Summarization of performance ----------------------------- ##
## ------------------------------------------------------------------------------------ ##
figures/misc/performance_summary.rds: \
$(multidsfigdir)/trueperformance/summary_trueperformance_sim.rds \
$(multidsfigdir)/truefpr/summary_truefpr_real.rds \
$(multidsfigdir)/timing/summary_timing_all.rds \
$(multidsfigdir)/de_characteristics/summary_de_characteristics_real.rds \
$(multidsfigdir)/runfailure/summary_runfailure_all.rds \
$(multidsfigdir)/orig_vs_mock/summary_orig_vs_mock_real.rds \
scripts/summarize_all_performances.R
	mkdir -p $(@D)
	$(R) "--args trueperformancerds='$(word 1,$^)' truefprrds='$(word 2,$^)' timingrds='$(word 3,$^)' fprbiasrds='$(word 4,$^)' failureraterds='$(word 5,$^)' origvsmockrds='$(word 6,$^)' outrds='$@'" scripts/summarize_all_performances.R Rout/summarize_all_performances.Rout

## ------------------------- Results for shiny application ---------------------------- ##
## ------------------------------------------------------------------------------------ ##
export_results/shiny_results.rds: \
$(multidsfigdir)/fracNA/summary_fracNA_real.rds \
$(multidsfigdir)/nbrdet/summary_nbrdet_real.rds \
$(multidsfigdir)/truefpr/summary_truefpr_real.rds \
$(multidsfigdir)/trueperformance/summary_trueperformance_sim.rds \
$(multidsfigdir)/timing/summary_timing_all.rds \
$(multidsfigdir)/de_characteristics/summary_de_characteristics_real.rds \
$(multidsfigdir)/orig_vs_mock/summary_orig_vs_mock_real.rds \
figures/misc/performance_summary.rds \
$(multidsfigdir)/crossmethod_consistency/summary_crossmethod_consistency_real.rds \
scripts/prepare_results_for_shiny.R
	mkdir -p $(@D)
	$(R) "--args fracnards='$(word 1,$^)' nbrgenesrds='$(word 2,$^)' type1errorrds='$(word 3,$^)' trueperfrds='$(word 4,$^)' timingrds='$(word 5,$^)' decharacrds='$(word 6,$^)' origvsmockrds='$(word 7,$^)' perfsummaryrds='$(word 8,$^)' crossmethodconsrds='$(word 9,$^)' outrds='$@'" scripts/prepare_results_for_shiny.R Rout/prepare_results_for_shiny.Rout