cleanup, scripts adjusted, improved figures

1 files changed, 26 insertions, 27 deletions

diff --git a/Makefile b/Makefile
index 41128b3..5b97564 100644
--- a/Makefile
+++ b/Makefile
@@ -15,10 +15,12 @@ TEMPLATE_FILE_LATEX   = pandoc-scholar.latex
 
 # crossvalidations
 
-CV_DIR = 10-fold-crossvalidations/
+CV_DIR = crossvalidations/
+LAZAR_MODELS_DIR = ../lazar/models/
+LAZAR_PREDICTIONS_DIR = ../lazar/predictions/
 
-LAZAR_MP2D_CONFUSION_MATRIX_DIR = $(CV_DIR)mp2d/lazar/crossvalidation/confusion_matrices/
-LAZAR_CDK_CONFUSION_MATRIX_DIR = $(CV_DIR)cdk/lazar/crossvalidation/confusion_matrices/
+LAZAR_MP2D_CONFUSION_MATRIX_DIR = $(LAZAR_MODELS_DIR)mutagenicity-mp2d/crossvalidation/confusion-matrices/
+LAZAR_CDK_CONFUSION_MATRIX_DIR = $(LAZAR_MODELS_DIR)mutagenicity-cdk/crossvalidation/confusion-matrices/
 TENSORFLOW_MP2D_CV_DIR = $(CV_DIR)mp2d/tensorflow/
 TENSORFLOW_CDK_CV_DIR = $(CV_DIR)cdk/tensorflow/
 
@@ -54,7 +56,6 @@ CV_SUMMARY = $(CV_DIR)summary.yaml
 # PA predictions
 
 PA_DIR = pyrrolizidine-alkaloids/
-PA_DATA_DIR = data/pyrrolizidine-alkaloids/
 
 PA_MP2D_DIR = $(PA_DIR)mp2d/
 PA_CDK_DIR = $(PA_DIR)cdk/
@@ -82,8 +83,8 @@ PA_CDK_TENSORFLOW_PREDICTIONS = $(addprefix $(PA_CDK_TENSORFLOW_DIR), \
 )
 
 PA_PREDICTIONS = \
-	$(PA_MP2D_LAZAR_DIR)pa-mp2d-predictions.csv \
-	$(PA_CDK_LAZAR_DIR)pa-cdk-predictions.csv \
+	$(PA_MP2D_LAZAR_DIR)predictions\
+	$(PA_CDK_LAZAR_DIR)predictions \
 	$(PA_MP2D_TENSORFLOW_PREDICTIONS) \
 	$(PA_CDK_TENSORFLOW_PREDICTIONS)
 
@@ -95,13 +96,9 @@ TABLES = $(addprefix tables/, \
 	lazar-summary.csv \
 	tensorflow-summary.csv \
 	pa-tab.tex \
-	pa-summary.csv \
 )
 
-FIGURES = $(addprefix figures/, \
-	roc.png \
-	tsne-mp2d.png \
-	tsne-cdk.png \
+PA_FIGURES = $(addprefix figures/, \
 	Dehydropyrrolizidine.png \
 	Diester.png \
 	Macrocyclic.diester.png \
@@ -113,6 +110,8 @@ FIGURES = $(addprefix figures/, \
 	Tertiary.PA.png \
 )
 
+FIGURES = figures/roc.png figures/tsne-mp2d.png figures/tsne-cdk.png $(PA_FIGURES)
+
 SUMMARY = summary.yaml
 
 all: mutagenicity.pdf 
@@ -126,15 +125,13 @@ mutagenicity.mustache.md: $(SUMMARY) mutagenicity.md $(TABLES) $(FIGURES)
 figures/tsne-cdk.png: figures/tsne-cdk.csv
 	Rscript scripts/tsne-cdk.R
 	
-# TODO: filtered CDK descriptors
-figures/tsne-cdk.csv: data/training/GenoTox-database.csv data/pyrrolizidine-alkaloids/PA-Padel-2D_m2.csv
+figures/tsne-cdk.csv:  mutagenicity/cdk/mutagenicity-mod-2.new.csv pyrrolizidine-alkaloids/PA-Padel-2D_m2.csv
 	scripts/cdk-descriptors.rb $^ > $@
 	
 figures/tsne-mp2d.png: figures/tsne-mp2d.csv
 	Rscript scripts/tsne-mp2d.R
 	
-# TODO: exported fingerprints
-figures/tsne-mp2d.csv: 10-fold-crossvalidations/mp2d/lazar/independent_variables
+figures/tsne-mp2d.csv: $(LAZAR_MODELS_DIR)mutagenicity-mp2d/independent-variables
 	scripts/mp2d-distances.rb > figures/tsne-mp2d.csv
 
 figures/roc.png: figures/roc.csv
@@ -143,6 +140,9 @@ figures/roc.png: figures/roc.csv
 figures/roc.csv: $(CV_SUMMARY)
 	scripts/summary2roc.rb $< > $@
 
+$(PA_FIGURES): tables/pa-table.csv
+	scripts/pa-groups.R
+
 # tables
 
 tables/pa-summary.csv: $(PA_SUMMARY)
@@ -170,15 +170,14 @@ $(PA_SUMMARY): tables/pa-table.csv
 
 # PA lazar predictions
 
-# TODO move to script dir, generate independent_variables from data
-$(PA_CDK_LAZAR_DIR)pa-cdk-predictions.csv: $(PA_CDK_LAZAR_DIR)pa_independent_variables
-	../lazar/bin/batch_padel_classification.rb 10-fold-crossvalidations/lazar-pa-cdk $< > $@
+$(PA_DIR)pa-canonical-smiles: $(PA_DIR)180920_PA_complete_SMILES.csv
+	scripts/pa-smiles.rb $< | obabel -ismi - -ocan | tr -d "\t" > $@
 
-$(PA_MP2D_LAZAR_DIR)pa-mp2d-predictions.csv: $(PA_DATA_DIR)pa-smiles.csv
-	../lazar/bin/batch_fingerprint_classification.rb ../lazar/models/mutagenicity $< > $@
+$(PA_CDK_LAZAR_DIR)predictions: $(LAZAR_PREDICTIONS_DIR)pa-cdk/predictions 
+	cp $< $@
 
-$(PA_DATA_DIR)pa-smiles.csv: $(PA_DATA_DIR)180920_PA_complete_SMILES.csv
-	cut -f1,4 -d ';' $< | sed 's/;/,/' > $@
+$(PA_MP2D_LAZAR_DIR)predictions: $(LAZAR_PREDICTIONS_DIR)pa-mp2d/predictions 
+	cp $< $@
 
 # crossvalidation summary
 
@@ -222,17 +221,17 @@ $(CONFUSION_MATRICES_DIR)tensorflow-svm-mp2d.csv: $(TENSORFLOW_MP2D_CV_DIR)pred.
 
 ### cdk
 
-$(CONFUSION_MATRICES_DIR)tensorflow-lr-cdk.csv: $(TENSORFLOW_CDK_CV_DIR)pred.lr.v4.csv
+$(CONFUSION_MATRICES_DIR)tensorflow-lr-cdk.csv: $(TENSORFLOW_CDK_CV_DIR)pred.lr.v4.norm.csv
 	scripts/cv-tensorflow-confusion-matrix.rb $< > $@
 
-$(CONFUSION_MATRICES_DIR)tensorflow-lr2-cdk.csv: $(TENSORFLOW_CDK_CV_DIR)pred.lr2.v4.csv
+$(CONFUSION_MATRICES_DIR)tensorflow-lr2-cdk.csv: $(TENSORFLOW_CDK_CV_DIR)pred.lr2.norm.v4.csv
 	scripts/cv-tensorflow-confusion-matrix.rb $< > $@
 
-$(CONFUSION_MATRICES_DIR)tensorflow-nn-cdk.csv: $(TENSORFLOW_CDK_CV_DIR)pred.nn.v4.csv
+$(CONFUSION_MATRICES_DIR)tensorflow-nn-cdk.csv: $(TENSORFLOW_CDK_CV_DIR)pred.nn.v4.norm.csv
 	scripts/cv-tensorflow-confusion-matrix.rb $< > $@
 
-$(CONFUSION_MATRICES_DIR)tensorflow-rf-cdk.csv: $(TENSORFLOW_CDK_CV_DIR)pred.rf.v4.csv
+$(CONFUSION_MATRICES_DIR)tensorflow-rf-cdk.csv: $(TENSORFLOW_CDK_CV_DIR)pred.rf.norm.v4.csv
 	scripts/cv-tensorflow-confusion-matrix.rb $< > $@
 
-$(CONFUSION_MATRICES_DIR)tensorflow-svm-cdk.csv: $(TENSORFLOW_CDK_CV_DIR)pred.svm.v4.csv
+$(CONFUSION_MATRICES_DIR)tensorflow-svm-cdk.csv: $(TENSORFLOW_CDK_CV_DIR)pred.svm.norm.v4.csv
 	scripts/cv-tensorflow-confusion-matrix.rb $< > $@