fig.cap and echo in markdown

[Gib Hemani]

I am trying to add figure captions to plots in markdown, but I also want to set echo=FALSE. It seems that I can have figure captions with echo, or no figure captions without echo. e.g. This will produce no figure captions

# A minimal R Markdown example
A _paragraph_ here. A code chunk below (remember the three backticks):
```{r, fig.cap=c("hello", "bye"), echo=FALSE}
plot(1:10)
hist(rnorm(1000))
```

but this one will produce figure captions:

# A minimal R Markdown example
A _paragraph_ here. A code chunk below (remember the three backticks):
```{r, fig.cap=c("hello", "bye"), echo=TRUE}
plot(1:10)
hist(rnorm(1000))
```

Any idea how I can get figure captions, but without echo?

Many thanks

[Carl Boettiger]

Hi Gib,

Interesting! Looks like there are actually several problems here, most having very little to do with echo but more to do with markdown parsing. 

Recall knitr turns .Rmd to .md; other tools turn it to html. Note that the .md files created in your examples work as expected, the figure caption follows the Pandoc convention in the md, . 

Look closely though, and you'll also notice in your .md file that you are not starting a new line before either figure, your output markdown looks like: 

# A minimal R Markdown example
A _paragraph_ here. A code chunk below (remember the three backticks):

 

Pandoc interprets those figures as "inline" figures, which don't get captions. If you want figures with captions, it seems like you have to give each it's own block (and skip a line before starting a chunk!)

# A minimal R Markdown example

A _paragraph_ here. A code chunk below (remember the three backticks):

```{r, fig.cap=c("hello"), echo=FALSE}

plot(1:10)

```

```{r, fig.cap=c("bye"), echo=FALSE}

hist(rnorm(1000))

```

Use pandoc to compile: pandoc -s file.md -o file.html and voila, you have captions.  

Things get more complicated if you're using RStudio's html button.  Briefly, recall that the current RStudio doesn't use pandoc to generate HTML, but a different markdown flavor which ignores the pandoc-style captions.  The preview/pre-release version of RStudio (0.98.932) does use pandoc, but turns captions off by default to avoid lots of "unnamed-chunk-2" captions.  

(You can turn captions on for pdfs with fig_caption: true argument in the yaml, but I don't see how to turn them on for html when using the RStudio button/rmarkdown::render).  

 I note that "echo" doesn't have any effect on the html captions once you have skipped lines appropriately.  

HTH,

Carl

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Carl Boettiger
UC Santa Cruz
http://carlboettiger.info/

[Yihui Xie]

Yes, Carl's explanation is absolutely correct. You need ![]() in a
separate paragraph to get figure captions in HTML, as documented here:
http://johnmacfarlane.net/pandoc/README.html#images

The trick here is to add some line breaks between the two images:

---
output:
html_document:
fig_caption: yes
---

# A minimal R Markdown example

A _paragraph_ here.

```{r, fig.cap=c("hello", "bye"), echo=FALSE, fig.retina=1}
plot(1:10)
cat('\n\n')
hist(rnorm(1000))
```

Note the chunk option fig.retina=1: without it, rmarkdown::render()
will generate plots for Retina displays, which means the plots are
written in raw <img> tags instead of ![](), and Pandoc will not be
able to generate figure captions in that case.

Regards,
Yihui
--
Yihui Xie <xiey...@gmail.com>
Web: http://yihui.name

[Yihui Xie]

I forgot to mention that you can also set the fig.retina option
globally, either through opts_chunk$set(fig.retina = 1), or in the
YAML metadata, e.g.

---
output:
html_document:
fig_caption: yes

fig_retina: 1

---

# A minimal R Markdown example

A _paragraph_ here.

```{r, fig.cap=c("hello", "bye"), echo=FALSE}

plot(1:10)
cat('\n\n')
hist(rnorm(1000))
```

Regards,
Yihui
--
Yihui Xie <xiey...@gmail.com>
Web: http://yihui.name

[Gib Hemani]

Dear Carl and Yihui

Very grateful for your responses, thanks for the explanations it all makes sense now =]

Knitr is cool

Gib