Generating a report using Rmd and bookdown

After moving to Latex, probably the next step is to generate the paper directly under R, or at least draft report.


  • Use R Studio
  • Install the bookdown library.
  • Generate html version of the Rmd file that has been used to generate the figures.
  • Locate in which directory they are (usually File_Name_files/figure-html/)
  • In the header of the Rmd file use the following code (YAML) this will use the bookdonw extension and allow to generate both html and
title: "My title"
author: "Me myself"
date: '`r format(Sys.time(), "%d %m %Y")`'
    number_sections: TRUE
    fig_caption: TRUE
    toc: false
    toc_depth: 1
    number_sections: TRUE
    fig_caption: TRUE
    toc: false


  • If you want to have the figures at the same place than the text, use HTML output, if this is not critical use pdf.
  • Give a name to each chunk that generate the figures because this name will be given to the png figures (e.g. abundant_species-1.png for a chunk named r abundant_species). It is better to use - than _ because _ will cause problem in Latex
  • Use the following code for inserting the figures in the reports
{r treemap,  fig.cap="Overall euk composition",  fig.align = "center", out.width ="50%"}
 knitr::include_graphics("Metabarcoding_Singapore_ASV_files/figure-html/treemap-1.png", dpi=72)
  • Important points
    • r treemap - This figure can then be referenced as (Figure \@ref(fig:treemap))
    • fig.cap="Overall euk composition" - This will the caption of the figure
    • out.width ="50%" - This is the best way to control the output and will work both with HTML and pdf