Makefile and scripts cleanup; lazar, R and tensorflow tables

1 files changed, 42 insertions, 90 deletions

diff --git a/Makefile b/Makefile
index 8b39538..b2a4708 100644
--- a/Makefile
+++ b/Makefile
@@ -7,122 +7,69 @@ ARTICLE_FILE          = mutagenicity.mustache.md
 PANDOC_SCHOLAR_PATH   = pandoc-scholar
 OUTFILE_PREFIX        = mutagenicity
 DEFAULT_EXTENSIONS    = pdf #latex docx html #odt epub
-#PANDOC_WRITER_OPTIONS = --filter=panpipe --filter=pandoc-placetable --filter=pandoc-citeproc -M tmpvar=test
 PANDOC_WRITER_OPTIONS = --filter=pandoc-placetable --filter=pandoc-crossref --filter=pandoc-citeproc
 TEMPLATE_FILE_LATEX   = pandoc-scholar.latex
 
-# Lazar
-
-LAZAR_DIR = ../lazar
-LAZAR_MODEL_DIR = $(LAZAR_DIR)/models/mutagenicity
-LAZAR_PADEL_MODEL_DIR = $(LAZAR_DIR)/models/mutagenicity-padel
-LAZAR_SUMMARY_DIR = $(LAZAR_MODEL_DIR)/crossvalidation/summaries
-LAZAR_PADEL_SUMMARY_DIR = $(LAZAR_PADEL_MODEL_DIR)/crossvalidation/summaries
-LAZAR_CONFUSION_MATRIX_DIR = $(LAZAR_MODEL_DIR)/crossvalidation/confusion_matrices
-LAZAR_PADEL_CONFUSION_MATRIX_DIR = $(LAZAR_PADEL_MODEL_DIR)/crossvalidation/confusion_matrices
-
 # Experiments
 
-SUMMARIES_DIR = 10-fold-crossvalidations/summaries
-CONFUSION_MATRICES_DIR = 10-fold-crossvalidations/confusion-matrices
+LAZAR_CONFUSION_MATRIX_DIR = 10-fold-crossvalidations/lazar/crossvalidation/confusion_matrices
+LAZAR_PADEL_CONFUSION_MATRIX_DIR = 10-fold-crossvalidations/lazar-padel/crossvalidation/confusion_matrices
 R_CV_DIR = 10-fold-crossvalidations/R
 TENSORFLOW_CV_DIR = 10-fold-crossvalidations/tensorflow
 
-#TABLES = tables/r-summary.csv tables/tf-summary.csv tables/lazar-summary.csv tables/R-SVM.csv tables/R-RF.csv tables/R-DL.csv tables/tensorflow-all.csv tables/tensorflow-selected.csv tables/lazar-all.csv tables/lazar-high-confidence.csv tables/lazar-padel-all.csv tables/lazar-padel-high-confidence.csv
-TABLES = tables/R-SVM.csv tables/R-RF.csv tables/R-DL.csv tables/tensorflow-all.csv tables/tensorflow-selected.csv tables/lazar-all.csv tables/lazar-high-confidence.csv tables/lazar-padel-all.csv tables/lazar-padel-high-confidence.csv #tables/pred.rf.v3.csv tables/pred.lr.v3.csv tables/pred.lr2.v3.csv tables/pred.nn.v3.csv
-
-R_SUMMARIES = $(SUMMARIES_DIR)/R-SVM.json $(SUMMARIES_DIR)/R-RF.json $(SUMMARIES_DIR)/R-DL.json
-TF_SUMMARIES = $(SUMMARIES_DIR)/tensorflow-all.json $(SUMMARIES_DIR)/tensorflow-selected.json $(SUMMARIES_DIR)/pred.lr.v3.json $(SUMMARIES_DIR)/pred.lr2.v3.json $(SUMMARIES_DIR)/pred.nn.v3.json $(SUMMARIES_DIR)/pred.rf.v3.json 
-LAZAR_SUMMARIES = $(SUMMARIES_DIR)/lazar-all.json $(SUMMARIES_DIR)/lazar-high-confidence.json $(SUMMARIES_DIR)/lazar-padel-all.json $(SUMMARIES_DIR)/lazar-padel-high-confidence.json
+CONFUSION_MATRICES_DIR = 10-fold-crossvalidations/confusion-matrices
+CONFUSION_MATRICES = $(CONFUSION_MATRICES_DIR)/R-SVM.csv $(CONFUSION_MATRICES_DIR)/R-RF.csv $(CONFUSION_MATRICES_DIR)/R-DL.csv $(CONFUSION_MATRICES_DIR)/lazar-all.csv $(CONFUSION_MATRICES_DIR)/lazar-high-confidence.csv $(CONFUSION_MATRICES_DIR)/lazar-padel-all.csv $(CONFUSION_MATRICES_DIR)/lazar-padel-high-confidence.csv  $(CONFUSION_MATRICES_DIR)/tensorflow-lr.v3.csv $(CONFUSION_MATRICES_DIR)/tensorflow-lr2.v3.csv $(CONFUSION_MATRICES_DIR)/tensorflow-nn.v3.csv $(CONFUSION_MATRICES_DIR)/tensorflow-rf.v3.csv 
 
-#SUMMARIES = $(R_SUMMARIES) $(TF_SUMMARIES) $(LAZAR_SUMMARIES)
+CV_SUMMARY = 10-fold-crossvalidations/summary.yaml
+TABLES = tables/lazar-summary.csv tables/r-summary.csv tables/tensorflow-summary.csv
+FIGURES = figures/roc.png figures/tsne-mp2d.png figures/tsne-padel.png #figures/pa-predictions.png
 
-CONFUSION_MATRICES = $(CONFUSION_MATRICES_DIR)/R-SVM.csv $(CONFUSION_MATRICES_DIR)/R-RF.csv $(CONFUSION_MATRICES_DIR)/R-DL.csv $(CONFUSION_MATRICES_DIR)/tensorflow-all.csv $(CONFUSION_MATRICES_DIR)/tensorflow-selected.csv $(CONFUSION_MATRICES_DIR)/lazar-all.csv $(CONFUSION_MATRICES_DIR)/lazar-high-confidence.csv $(CONFUSION_MATRICES_DIR)/lazar-padel-all.csv $(CONFUSION_MATRICES_DIR)/lazar-padel-high-confidence.csv  $(CONFUSION_MATRICES_DIR)/tensorflow-lr.v3.csv $(CONFUSION_MATRICES_DIR)/tensorflow-lr2.v3.csv $(CONFUSION_MATRICES_DIR)/tensorflow-nn.v3.csv $(CONFUSION_MATRICES_DIR)/tensorflow-rf.v3.csv 
-DATA = data/mutagenicity.sdf data/mutagenicity.csv data/mutagenicity-fingerprints.csv
-FIGURES = figures/roc.png figures/tsne-mp2d.png figures/tsne-padel.png
+# manuscript
 
-all: $(DATA) $(TABLES) $(FIGURES) mutagenicity.pdf 
+all: $(TABLES) $(FIGURES) mutagenicity.pdf 
 include $(PANDOC_SCHOLAR_PATH)/Makefile
-export: $(DATA) 
 
-mutagenicity.mustache.md: results.yaml mutagenicity.md $(FIGURES)
+mutagenicity.mustache.md: $(CV_SUMMARY) mutagenicity.md $(TABLES) $(FIGURES)
 	mustache $^ > $@
 
 # figures
+
 figures/tsne-padel.png: figures/tsne-padel.csv
-	scripts/padel-tsne.R
+	scripts/tsne-padel.R
 	
 figures/tsne-padel.csv: data/GenoTox-database.csv pyrrolizidine-alkaloids/PA-Padel-2D_m2.csv
 	scripts/padel-descriptors.rb $^ > $@
 	
 figures/tsne-mp2d.png: figures/tsne-mp2d.csv
-	scripts/mp2d-tsne.R
+	scripts/tsne-mp2d.R
 	
-figures/tsne-mp2d.csv: ../lazar/models/mutagenicity/independent_variables
+figures/tsne-mp2d.csv: 10-fold-crossvalidations/lazar/independent_variables
 	scripts/mp2d-distances.rb > figures/tsne-mp2d.csv
 
-figures/roc.png: figures/results.csv
+figures/roc.png: figures/roc.csv
 	scripts/roc.R 
 
-figures/results.csv: results.yaml
+figures/roc.csv: $(CV_SUMMARY)
 	scripts/results2csv.rb $< > $@
 
 # tables
 
-tables/r-summary.csv: $(R_SUMMARIES)
-	scripts/summaries2table.rb $^ > $@
-
-tables/tf-summary.csv: $(TF_SUMMARIES)
-	scripts/summaries2table.rb $^ > $@
+tables/lazar-summary.csv: $(CV_SUMMARY)
+	scripts/summaries2table.rb lazar > $@
 
-tables/lazar-summary.csv: $(LAZAR_SUMMARIES)
-	scripts/summaries2table.rb $^ > $@
+tables/r-summary.csv: $(CV_SUMMARY)
+	scripts/summaries2table.rb R > $@
 
-tables/%.csv: $(CONFUSION_MATRICES_DIR)/%.csv
-	scripts/confusion-matrix2table.rb $< > $@
+tables/tensorflow-summary.csv: $(CV_SUMMARY)
+	scripts/summaries2table.rb tensorflow > $@
 
-# summaries
+# crossvalidation summary
 
-#$(SUMMARIES_DIR)/results.json: $(SUMMARIES)
-	#scripts/results.rb $^ > $@
-
-#$(SUMMARIES_DIR)/%.json: $(CONFUSION_MATRICES_DIR)/%.csv
-	#scripts/confusion-matrix-summary.rb $< > $@
-
-results.yaml: $(CONFUSION_MATRICES)
+$(CV_SUMMARY): $(CONFUSION_MATRICES)
 	scripts/confusion-matrix-summary.rb $^ > $@
 
 # confusion matrices
 
-## tensorflow
-$(CONFUSION_MATRICES_DIR)/tensorflow-selected.csv: $(TENSORFLOW_CV_DIR)/pred.sorted.csv
-	scripts/cv-tensorflow-confusion-matrix.rb $< > $@
-
-$(CONFUSION_MATRICES_DIR)/tensorflow-all.csv: $(TENSORFLOW_CV_DIR)/pred_ext.sorted.csv
-	scripts/cv-tensorflow-confusion-matrix.rb $< > $@
-
-$(CONFUSION_MATRICES_DIR)/tensorflow-lr.v3.csv: $(TENSORFLOW_CV_DIR)/pred.lr.v3.sorted.csv
-	scripts/cv-tensorflow-confusion-matrix.rb $< > $@
-
-$(CONFUSION_MATRICES_DIR)/tensorflow-lr2.v3.csv: $(TENSORFLOW_CV_DIR)/pred.lr2.v3.sorted.csv
-	scripts/cv-tensorflow-confusion-matrix.rb $< > $@
-
-$(CONFUSION_MATRICES_DIR)/tensorflow-nn.v3.csv: $(TENSORFLOW_CV_DIR)/pred.nn.v3.sorted.csv
-	scripts/cv-tensorflow-confusion-matrix.rb $< > $@
-
-$(CONFUSION_MATRICES_DIR)/tensorflow-rf.v3.csv: $(TENSORFLOW_CV_DIR)/pred.rf.v3.sorted.csv
-	scripts/cv-tensorflow-confusion-matrix.rb $< > $@
-
-## R
-$(CONFUSION_MATRICES_DIR)/R-SVM.csv: $(R_CV_DIR)/Sgl-Observations-SVM.csv
-	scripts/cv-r-confusion-matrix.rb $< > $@
-
-$(CONFUSION_MATRICES_DIR)/R-RF.csv: $(R_CV_DIR)/Sgl-Observations-RF.csv
-	scripts/cv-r-confusion-matrix.rb $< > $@
-
-$(CONFUSION_MATRICES_DIR)/R-DL.csv: $(R_CV_DIR)/Sgl-Observations-DL.csv
-	scripts/cv-r-confusion-matrix.rb $< > $@
-
 ## lazar
 $(CONFUSION_MATRICES_DIR)/lazar-all.csv: $(LAZAR_CONFUSION_MATRIX_DIR)
 	cp $</all $@
@@ -136,21 +83,26 @@ $(CONFUSION_MATRICES_DIR)/lazar-padel-all.csv: $(LAZAR_PADEL_CONFUSION_MATRIX_DI
 $(CONFUSION_MATRICES_DIR)/lazar-padel-high-confidence.csv: $(LAZAR_PADEL_CONFUSION_MATRIX_DIR)
 	cp $</high_confidence $@
 
-# exports
+## R
+$(CONFUSION_MATRICES_DIR)/R-SVM.csv: $(R_CV_DIR)/Sgl-Observations-SVM.csv
+	scripts/cv-r-confusion-matrix.rb $< > $@
 
-data/mutagenicity-fingerprints.csv: $(LAZAR_DIR)/models/mutagenicity
-	$(LAZAR_DIR)/bin/export-fingerprints.rb $< > $@
+$(CONFUSION_MATRICES_DIR)/R-RF.csv: $(R_CV_DIR)/Sgl-Observations-RF.csv
+	scripts/cv-r-confusion-matrix.rb $< > $@
 
-data/mutagenicity.csv: $(LAZAR_DIR)/models/mutagenicity/Mutagenicity-Salmonella_typhimurium.csv
-	cp $< > $@
+$(CONFUSION_MATRICES_DIR)/R-DL.csv: $(R_CV_DIR)/Sgl-Observations-DL.csv
+	scripts/cv-r-confusion-matrix.rb $< > $@
 
-data/mutagenicity.sdf: $(LAZAR_DIR)/models/mutagenicity/Mutagenicity-Salmonella_typhimurium.csv
-	$(LAZAR_DIR)/bin/export-sdf.rb $< > $@
-	
-# lazar models and crossvalidations
+## tensorflow
+$(CONFUSION_MATRICES_DIR)/tensorflow-lr.v3.csv: $(TENSORFLOW_CV_DIR)/pred.lr.v3.sorted.csv
+	scripts/cv-tensorflow-confusion-matrix.rb $< > $@
 
-$(LAZAR_SUMMARY_DIR):
-	make -C $(LAZAR_MODEL_DIR)
+$(CONFUSION_MATRICES_DIR)/tensorflow-lr2.v3.csv: $(TENSORFLOW_CV_DIR)/pred.lr2.v3.sorted.csv
+	scripts/cv-tensorflow-confusion-matrix.rb $< > $@
+
+$(CONFUSION_MATRICES_DIR)/tensorflow-nn.v3.csv: $(TENSORFLOW_CV_DIR)/pred.nn.v3.sorted.csv
+	scripts/cv-tensorflow-confusion-matrix.rb $< > $@
+
+$(CONFUSION_MATRICES_DIR)/tensorflow-rf.v3.csv: $(TENSORFLOW_CV_DIR)/pred.rf.v3.sorted.csv
+	scripts/cv-tensorflow-confusion-matrix.rb $< > $@
 
-$(LAZAR_PADEL_SUMMARY_DIR):
-	make -C $(LAZAR_PADEL_MODEL_DIR)