consolidate references

Author: sathomas

combined.docx

@@ -0,0 +1,36 @@
+#!/bin/zsh
+# Shell script to convert source files into a MS-Word
+# document. Most of the heavy lifting done by pandoc:
+#   https://pandoc.org
+# Last tested with v3.1.
+#
+# Equation, Figure, and Table numbering/cross references
+# handled by pandoc-crossref:
+#   https://lierdakil.github.io/pandoc-crossref/#citeproc-and-pandoc-crossref
+# Last tested with v0.3.15.1.
+
+# Cleanup markdown before passing to pandoc
+# - missing italics for genes and QS systems
+# - unicode glyphs to markdown subscripts
+# - GitHub-friendly subscripts/superscripts to real markdown
+
+cat paper.md supporting.md | sed \
+    -e 's/ lasB/ _lasB_/g' \
+    -e 's/ lasI/ _lasI_/g' \
+    -e 's/ lasR/ _lasR_/g' \
+    -e 's/ rhlI/ _rhlI_/g' \
+    -e 's/ rhlR/ _rhlR_/g' \
+    -e 's/ las/ _las_/g' \
+    -e 's/ rhl/ _rhl_/g' \
+    -e 's/C₄‑HSL/C~4~‑HSL/g' \
+    -e 's/3‑oxo‑C₁₂‑HSL/3‑oxo‑C~12~‑HSL/g' \
+    -e 's/<\/\{0,1\}sub>/~/g' \
+    -e 's/<\/\{0,1\}sup>/^/g' \
+| pandoc \
+    --from markdown \
+    --filter pandoc-crossref \
+    --citeproc \
+    --csl plos-biology.csl \
+    --bibliography "Bibliography (BibTeX).bib" \
+    --reference-doc=reference.docx \
+    --output "combined.docx"

generate_combined.sh

@@ -67,7 +67,7 @@ Table: rhlr {#tbl:rhlr}
 
 Gene expression data for *lasI,* *rhlI,* and *lasB* was collected every hour for a 24-hour period. Observations used for analysis were limited to a two-hour window that contained the peak expression level for each gene. Figures S[-@fig:lasi_time], S[-@fig:rhli_time], and S[-@fig:lasb_time] show the full time course of expression levels and highlight the intervals used for analysis. Those windows were 8–10 hours, 3–5 hours, and 4–6 hours for *lasI,* *rhlI,* and *lasB,* respectively.
 
-![lasi_time](Figures/figs1_lasi_time.svg){#fig:lasi_time}
+![lasi_time](Figures/figs1_lasi_time.svg){#fig:lasi_time number=1}
 
 <div custom-style="Caption"><p>
 **Figure S[-@fig:lasi_time]. Expression level of _lasI_ over time course of experiment.** Shaded regions highlight peak expression and indicate two-hour period used in analysis. (The data underlying this Figure and the code used to analyze it can be found in https://doi.org/10.5281/zenodo.15808353.)