From 0611956316fd70c0e951b9e7a8aff41412db2443 Mon Sep 17 00:00:00 2001
From: Pariksheet Nanda <pariksheet.nanda@uconn.edu>
Date: Thu, 23 Mar 2017 10:28:44 -0400
Subject: [PATCH] ENH: Automate running the R scripts

---
 Makefile | 23 ++++++++++++++---------
 1 file changed, 14 insertions(+), 9 deletions(-)

diff --git a/Makefile b/Makefile
index b73c420..d750ff3 100644
--- a/Makefile
+++ b/Makefile
@@ -13,7 +13,7 @@ PYTHON := python
 RSCRIPT := Rscript
 TIME := command time --format "Completed in wall clock time [H:M:S]: %E"
 
-# Make rule sources and targets
+# Make rule sources, targets and helper functions
 SOURCES_img_raw := data/April_14_2016.tar.xz
 TARGETS_img_raw := data/April_14_2016
 SOURCES_img_zproj := $(TARGETS_img_raw)
@@ -53,12 +53,12 @@ $(CELLPROFILER_OPTS_COMMON) \
 --pipeline=$(SOURCES_cellprofiler_commands) \
 --run-headless
 endef
-SOURCES_signif_wells := $(TARGETS_cellprofiler_db)
+SOURCES_signif_wells := src/overlap-analysis.R $(TARGETS_cellprofiler_db)
 TARGETS_signif_wells := results/tables/rnai-p_values.csv
-SOURCES_plot_overlap := $(TARGETS_signif_wells)
-TARGETS_plot_overlap := $(addsuffix results/plots/,)
-SOURCES_plot_plates := $(TARGETS_signif_wells)
-TARGETS_plot_plates := $(addsuffix results/plots/,)
+SOURCES_plot_overlap := src/plots.R $(TARGETS_signif_wells)
+TARGETS_plot_overlap := results/plots/rnai-hist-signif.png
+SOURCES_plot_plates := src/plot-plates.R $(TARGETS_signif_wells)
+TARGETS_plot_plates := results/plots/stddev-scatter.png
 TARGETS_plots := $(TARGETS_plot_overlap) $(TARGETS_plot_plates)
 
 # Functions
@@ -70,7 +70,7 @@ $(foreach path,$1,$(shell echo -n $(path) | sed 's#\(.*\)\.#\1%##'))
 endef
 
 .PHONY : all
-all : z-projection cellprofiler plots ## (Default) Run full pipeline from image processing to plots.
+all : z-projection cellprofiler stats plots ## (Default) Run full pipeline from image processing to plots.
 
 # Self-documenting help modified from
 # https://gist.github.com/prwhite/8168133#gistcomment-1737630
@@ -108,14 +108,19 @@ gui-cellprofiler : $(SOURCES_cellprofiler) ## Interactively run CellProfiler.
 $(TARGETS_img_filelist) : $(abspath $(SOURCES_img_filelist))
 	find $< -type f | sort > $@
 
+.PHONY : stats
+stats : $(TARGETS_signif_wells)	## Find significant wells from cellprofiler measurements.
+$(TARGETS_signif_wells) : $(SOURCES_signif_wells)
+	cd $(<D); $(RSCRIPT) $(<F)
+
 .PHONY : plots
 plots : $(TARGETS_plots)
 
 $(TARGETS_plot_overlap) : $(SOURCES_plot_overlap)
-	$(RSCRIPT) src/plots.R
+	cd $(<D); $(RSCRIPT) $(<F)
 
 $(TARGETS_plot_plates) : $(SOURCES_plot_plates)
-	$(RSCRIPT) src/plot-plates.R
+	cd $(<D); $(RSCRIPT) $(<F)
 
 .PHONY : clean-all
 clean-all :			## Delete all output.