add bibliography

_bookdown.yml

@@ -14,7 +14,9 @@ rmd_files: [
   #"bargraphs_logy.Rmd",
   "overlapping_points.Rmd",
 
-  "notes.Rmd"
+  "notes.Rmd",
+
+  "references.Rmd"
 ]
 
 before_chapter_script: "_common.R"

background_grids.Rmd

@@ -126,7 +126,7 @@ iris %>%
 stamp_good(plot_grid(NULL, iris_plot + theme_pf_grid(), NULL, nrow=1, rel_widths=c(0.02, 1, 0.04)))
 ```
 
-For figures where the relevant comparison is the $x=y$ line, I prefer to draw a diagonal line rather than a grid. For example, if we compare two sets of correlations, we can see immediately which correlations are systematically stronger (figure adapted from **Echave et al, need to add reference here**):
+For figures where the relevant comparison is the $x=y$ line, I prefer to draw a diagonal line rather than a grid. For example, consider the following figure, adapted from @Echave-et-al-2016, which compares two sets of correlations for 209 protein structures. By drawing the diagonal line, we can see immediately which correlations are systematically stronger:
 ```{r message=FALSE, warning=FALSE}
 cor_table = read_csv("datasets/Echave_et_al_2016_NRG_correlations.csv")
 nrg_plot <- ggplot(cor_table, aes(y=cor.RSA, x=-cor.WCN)) + 

bibliography.bib

@@ -0,0 +1,8 @@
+@article{Echave-et-al-2016,
+    author = {Echave, J. and Spielman, S. J. and Wilke, C. O.},
+    journal = {Nature Rev. Genet.},
+    pages = {109--121},
+    title = {Causes of evolutionary rate variation among protein sites},
+    volume = {17},
+    year = {2016}
+}

index.Rmd

@@ -4,6 +4,9 @@ author: "Claus O. Wilke"
 description: "A guide for making figures that look professional and are publication-ready."
 github-repo: clauswilke/professional_figures
 site: bookdown::bookdown_site
+bibliography: "bibliography.bib"
+biblio-style: "apalike"
+link-citations: true
 output:
   bookdown::gitbook: default
 ---

references.Rmd

@@ -0,0 +1 @@
+`r if (knitr:::is_html_output()) '# References {-}'`