Bookdown figure caption fails if too long in landscape?

Question

I have a plot which is large enough to require plotting landscape in what is otherwise a portrait document using (PDF) bookdown in RStudio. The figure has a lot going on, so the figure caption is quite long, and I cannot really reduce the text any further.

Here is example code I have been using:

```{r qtl-pleiotropy, out.extra='angle=90', fig.width=25/2.54, fig.height=16.9/2.54, 
     fig.cap="QTL for fruit number per reproductive plant (Fruits/RP), seed number per fruit (Seeds/fr), seed number per reproductive plant (Seeds/RP), seed mass (Sd mass) and survival (Surv). Arrows indicate most-likely QTL position with the 95% Bayesian credible intervals, and the effect of the Swedish genotype (upward: increased phenotype; downward: decreased phenotype) in Italy (red) and Sweden (blue). Open arrows show QTL with credible intervals >15.2cM. Labels on the right of chromosome indicate QTL with pleiotropic effects on components of fecundity (c), fecundity and survival (s) and fecundity and seed mass (m). Grey boxes indicate the range of colocalising QTL for a single trait across site-year combinations."}
hist(rnorm(100)
```

The problem is that this outputs a landscape plot, but the caption is rendered as body text in the PDF output (i.e. not as a figure caption):

\begin{figure} \caption{QTL for fruit number per reproductive plant (Fruits/RP), seed number per fruit (Seeds/fr), seed number per reproductive plant (Seeds/RP), seed mass (Sd mass) and survival (Surv). Arrows indicate most-likely QTL position with the 95% Bayesian credible intervals, and the effect of the Swedish genotype (upward: increased phenotype; downward: decreased phenotype) in Italy (red) and Sweden (blue). Open arrows show QTL with credible intervals >15.2cM. Labels on the right of chromosome indicate QTL with pleiotropic effects on components of fecundity (c), fecundity and survival (s) and fecundity and seed mass (m). Grey boxes indicate the range of colocalising QTL for a single trait across site-year combinations.} \end{figure}

If I do not use landscape (i.e. leave out the out.extra='angle=90'), this works. If I take a shorter chunk of the caption, it also renders correctly. This works, for example:

```{r qtl-pleiotropy, out.extra='angle=90', fig.width=25/2.54, fig.height=16.9/2.54, 
     fig.cap="Open arrows show QTL with credible intervals >15.2cM. Labels on the right of chromosome indicate QTL with pleiotropic effects on components of fecundity (c), fecundity and survival (s) and fecundity and seed mass (m). Grey boxes indicate the range of colocalising QTL for a single trait across site-year combinations."}
hist(rnorm(100))
```

Is there an upper bound on caption length when out.extra='angle=90'?

Can anyone suggest a work-around for this?

Answer 1

The problem is not caused by the length of the caption but by the unescaped %. The following works for me:

```{r qtl-pleiotropy1, out.extra='angle=90', fig.width=25/2.54, fig.height=16.9/2.54, fig.cap="QTL for fruit number per reproductive plant (Fruits/RP), seed number per fruit (Seeds/fr), seed number per reproductive plant (Seeds/RP), seed mass (Sd mass) and survival (Surv). Arrows indicate most-likely QTL position with the 95\\% Bayesian credible intervals, and the effect of the Swedish genotype (upward: increased phenotype; downward: decreased phenotype) in Italy (red) and Sweden (blue). Open arrows show QTL with credible intervals >15.2cM. Labels on the right of chromosome indicate QTL with pleiotropic effects on components of fecundity (c), fecundity and survival (s) and fecundity and seed mass (m). Grey boxes indicate the range of colocalising QTL for a single trait across site-year combinations."}
hist(rnorm(100))
```