diff options
Diffstat (limited to 'Makefile')
| -rw-r--r-- | Makefile | 66 |
1 files changed, 47 insertions, 19 deletions
@@ -7,7 +7,7 @@ ARTICLE_FILE = mutagenicity.mustache.md PANDOC_SCHOLAR_PATH = pandoc-scholar OUTFILE_PREFIX = mutagenicity -DEFAULT_EXTENSIONS = pdf +DEFAULT_EXTENSIONS = pdf docx PANDOC_WRITER_OPTIONS = --filter=pandoc-crossref --filter=pandoc-citeproc TEMPLATE_FILE_LATEX = pandoc-scholar.latex @@ -47,19 +47,26 @@ PA_SUMMARY = $(PA_DIR)summary.yaml # manuscript -PA_FIGURES = $(addprefix figures/, \ - Dehydropyrrolizidine.png \ - Diester.png \ - Macrocyclic.diester.png \ - Monoester.png \ - N.oxide.png \ - Otonecine.png \ - Platynecine.png \ - Retronecine.png \ - Tertiary.PA.png \ +TSNE_FIGURES = $(addprefix figures/tsne-, \ + mp2d-mutagenicity.png \ + cdk-mutagenicity.png \ + mp2d-lazar-high-confidence-classifications.png \ + mp2d-lazar-all-classifications.png \ + mp2d-rf-classifications.png \ + mp2d-lr-classifications.png \ + mp2d-lr2-classifications.png \ + mp2d-nn-classifications.png \ + mp2d-svm-classifications.png \ + cdk-lazar-high-confidence-classifications.png \ + cdk-lazar-all-classifications.png \ + cdk-rf-classifications.png \ + cdk-lr-classifications.png \ + cdk-lr2-classifications.png \ + cdk-nn-classifications.png \ + cdk-svm-classifications.png \ ) -FIGURES = figures/roc.png figures/tsne-mp2d-mutagenicity.png figures/tsne-cdk-mutagenicity.png $(PA_FIGURES) +FIGURES = figures/roc.png figures/pa-groups.png $(TSNE_FIGURES) DATA = data.yaml @@ -77,6 +84,18 @@ $(DATA): $(PA_SUMMARY) $(CV_SUMMARY) mutagenicity/mutagenicity.csv mutagenicity/ ## tsne +figures/tsne-mp2d-%.png: figures/tsne-mp2d-coordinates.csv figures/mp2d-% + Rscript scripts/tsne-classifications.R $^ $@ + +figures/mp2d-%-classifications: figures/tsne-mp2d-coordinates.csv crossvalidations/predictions/mp2d/%.csv pyrrolizidine-alkaloids/mp2d/%.csv + scripts/cv-pa-classifications.rb $^ > $@ + +figures/tsne-cdk-%.png: figures/tsne-cdk-coordinates.csv figures/cdk-% + Rscript scripts/tsne-classifications.R $^ $@ + +figures/cdk-%-classifications: figures/tsne-cdk-coordinates.csv crossvalidations/predictions/cdk/%.csv pyrrolizidine-alkaloids/cdk/%.csv + scripts/cv-pa-classifications.rb $^ > $@ + figures/tsne-%-mutagenicity.png: figures/tsne-%-coordinates.csv figures/tsne-%-mutagenicity.csv Rscript scripts/tsne-mutagenicity.R $^ $@ @@ -104,15 +123,18 @@ figures/tsne-mp2d-distances.csv: mutagenicity/mutagenicity-mp2d pyrrolizidine-al ## roc figures/roc.png: figures/roc.csv - Rscript scripts/roc.R + Rscript scripts/roc.R $< $@ figures/roc.csv: $(CV_SUMMARY) scripts/roc.rb $< > $@ ## pa predictions per group -$(PA_FIGURES): $(PA_DIR)pa-groups.csv $(PA_DIR)pa-predictions.csv - scripts/pa-groups.R $^ +figures/pa-groups.png: figures/pa-groups.csv + scripts/pa-groups.R $< $@ + +figures/pa-groups.csv: $(PA_DIR)pa-groups.csv $(PA_DIR)pa-predictions.csv + scripts/pa-groups.rb $^ > $@ # PA predictions @@ -136,12 +158,15 @@ $(PA_DIR)pa-predictions.csv: $(PA_PREDICTIONS) ## predictions -$(PA_DIR)%/lazar-all.csv: $(LAZAR_PREDICTIONS_DIR)pa-%/predictions +$(PA_DIR)%/lazar-all.csv: $(LAZAR_PREDICTIONS_DIR)pa-%/pa-%-prediction.csv scripts/lazar-pa-predictions.rb $< > $@ -$(PA_DIR)%/lazar-high-confidence.csv: $(LAZAR_PREDICTIONS_DIR)pa-%/predictions +$(PA_DIR)mp2d/lazar-high-confidence.csv: $(LAZAR_PREDICTIONS_DIR)pa-mp2d/pa-mp2d-prediction.csv scripts/lazar-pa-predictions.rb $< 0.5 > $@ +$(PA_DIR)cdk/lazar-high-confidence.csv: $(LAZAR_PREDICTIONS_DIR)pa-cdk/pa-cdk-prediction.csv + scripts/lazar-pa-predictions.rb $< 0.9 > $@ + $(PA_DIR)mp2d/%.csv: $(TENSORFLOW_PA_DIR)pred.%.v5-ext-ext-Padel-2D.csv $(PA_DIR)pa-cids.csv scripts/tensorflow-pa-predictions.rb $^ > $@ @@ -167,12 +192,15 @@ $(CONFUSION_MATRICES_DIR)%: $(CV_PREDICTIONS_DIR)% ## predictions -$(CV_PREDICTIONS_DIR)%/lazar-all.csv: $(LAZAR_MODELS_DIR)mutagenicity-% +$(CV_PREDICTIONS_DIR)%/lazar-all.csv: $(LAZAR_MODELS_DIR)mutagenicity-%/crossvalidation/predictions.csv scripts/lazar-cv-predictions.rb $< > $@ -$(CV_PREDICTIONS_DIR)%/lazar-high-confidence.csv: $(LAZAR_MODELS_DIR)mutagenicity-% +$(CV_PREDICTIONS_DIR)mp2d/lazar-high-confidence.csv: $(LAZAR_MODELS_DIR)mutagenicity-mp2d/crossvalidation/predictions.csv scripts/lazar-cv-predictions.rb $< 0.5 > $@ +$(CV_PREDICTIONS_DIR)cdk/lazar-high-confidence.csv: $(LAZAR_MODELS_DIR)mutagenicity-cdk/crossvalidation/predictions.csv + scripts/lazar-cv-predictions.rb $< 0.9 > $@ + $(CV_PREDICTIONS_DIR)mp2d/%.csv: $(TENSORFLOW_CV_DIR)pred.%.v4_ext.csv scripts/tensorflow-cv-predictions.rb $< > $@ |