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csoneson avatar csoneson commented on July 17, 2024 1

You can find the entire procedure to generate the results in the Makefile: https://github.com/csoneson/conquer_comparison/blob/master/Makefile. The specific lines that generate Figure 1 are

conquer_comparison/Makefile

Lines 722 to 730 in 3c93f77

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}))
, which in turn assumes that you have run

conquer_comparison/Makefile

Lines 541 to 549 in 3c93f77

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))))))
, following

conquer_comparison/Makefile

Lines 403 to 428 in 3c93f77

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))))
. All the scripts are also available in the GitHub repository.

from conquer_comparison.

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