R Markdown HTML Number Figures

Question

Does anyone know how to number the figures in the captions, for HTML format R Markdown script?

For PDF documents, the caption will say something like:

Answer 1

We can make use of pandoc-crossref, a filter that allows a cross-referencing of figures, tables, sections, and equations and works for all output format. The easiest way is to cat the figure label (in the form of {#fig:figure_label}) after each plot, although this requires echo=FALSE and results='asis'. Then we can reference a figure as we would a citation : [@fig:figure_label] produces fig. figure_number by default.

Here is a MWE:

---
output: 
  html_document:
    toc: true
    number_sections: true
    fig_caption: true
    pandoc_args: ["-F","pandoc-crossref"]
---

```{r}
knitr::opts_chunk$set(echo=FALSE,results='asis')

```


```{r plot1,fig.cap="This is plot one"}
x <- 1:10
y <- rnorm(10)
plot(x,y)
cat("{#fig:plot1}")

```

As we can see in [@fig:plot1]... whereas [@fig:plot2] shows...

```{r plot2, fig.cap="This is plot two"}
plot(y,x)
cat("{#fig:plot2}")

```

which produces (removing the graphics

PLOT1

Figure 1: This is plot one

As we can see in fig. 1… whereas fig. 2 shows…

PLOT2

Figure 2: This is plot two

See the pandoc-crossref readme for more options and customizations.

To install pandoc-crossref, assuming you have a haskell installation:

cabal update
cabal install pandoc-crossref