diff options
| author | Christoph Helma <helma@in-silico.ch> | 2020-10-20 21:23:48 +0200 |
|---|---|---|
| committer | Christoph Helma <helma@in-silico.ch> | 2020-10-20 21:23:48 +0200 |
| commit | 94f0aa4ecdb3e137590420c0bbd38d15108acec4 (patch) | |
| tree | 700d4b30e7ce64d6a64e3f0f71dfdb8d0a78c99c | |
| parent | 0b686f924a42105f2516aea44c27b6d3f75e1672 (diff) | |
Mustache fixed
| -rw-r--r-- | Makefile | 4 | ||||
| -rw-r--r-- | figures/roc.png | bin | 146544 -> 134226 bytes | |||
| -rw-r--r-- | mutagenicity.md | 7 | ||||
| -rw-r--r-- | mutagenicity.pdf | bin | 1846417 -> 1847966 bytes |
4 files changed, 7 insertions, 4 deletions
@@ -6,7 +6,7 @@ ARTICLE_FILE = mutagenicity.mustache.md PANDOC_SCHOLAR_PATH = pandoc-scholar OUTFILE_PREFIX = mutagenicity -DEFAULT_EXTENSIONS = pdf #latex docx html #odt epub +DEFAULT_EXTENSIONS = pdf #latex#docx html #odt epub PANDOC_WRITER_OPTIONS = --filter=pandoc-placetable --filter=pandoc-crossref --filter=pandoc-citeproc TEMPLATE_FILE_LATEX = pandoc-scholar.latex @@ -42,7 +42,7 @@ FIGURES = figures/roc.png figures/tsne-mp2d.png figures/tsne-padel.png all: $(TABLES) $(FIGURES) $(CV_SUMMARY) mutagenicity.pdf include $(PANDOC_SCHOLAR_PATH)/Makefile -mutagenicity.mustache.md: $(CV_SUMMARY) $(PA_SUMMARY) mutagenicity.md $(TABLES) $(FIGURES) +mutagenicity.mustache.md: $(CV_SUMMARY) mutagenicity.md $(TABLES) $(FIGURES) mustache $^ > $@ # figures diff --git a/figures/roc.png b/figures/roc.png Binary files differindex 24a9dfb..732299b 100644 --- a/figures/roc.png +++ b/figures/roc.png diff --git a/mutagenicity.md b/mutagenicity.md index d05cbc7..6abd497 100644 --- a/mutagenicity.md +++ b/mutagenicity.md @@ -514,13 +514,15 @@ Pyrrolizidine alkaloid mutagenicity predictions ----------------------------------------------- Mutagenicity predictions from all investigated models for 602 pyrrolizidine -alkaloids (PAs) are summarized in Table 4. A CSV table with all predictions can be +alkaloids (PAs) are shown in Table 4. A CSV table with all predictions can be downloaded from https://git.in-silico.ch/mutagenicity-paper/tables/pa-table.csv -**TODO** **Verena und Philipp** Koennt Ihr bitte stichprobenweise die Tabelle ueberpruefen, mir verrutscht bei der Auswertung immer gerne etwas. +**TODO** **Verena und Philipp** Koennt Ihr bitte stichprobenweise die Tabelle ueberpruefen \input{tables/pa-tab.tex} +@tbl:pa-summary summarises the number of positive and negative mutagenicity predictions for all investigated models. + ```{#tbl:pa-summary .table file="tables/pa-summary.csv" caption="Summary of pyrrolizidine alkaloid mutagenicity predictions"} ``` @@ -532,6 +534,7 @@ maintaining the high-dimensional distances of the objects. Similar objects are represented by nearby points and dissimilar objects are represented by distant points. + @fig:tsne-mp2d shows the t-SNE of pyrrolizidine alkaloids (PA) and the mutagenicity training data in MP2D space (Tanimoto/Jaccard similarity). {#fig:tsne-mp2d} diff --git a/mutagenicity.pdf b/mutagenicity.pdf Binary files differindex 9eaf590..af2434a 100644 --- a/mutagenicity.pdf +++ b/mutagenicity.pdf |
