How to add multiple figures across multiple pages in a chunk using knitr and RMarkdown?

Question

I am using a for loop to create multiple big figures across multiple pages in one chunk with knitr and rmarkdown. It works fine for word and html outputs, but has one problem in pdf output.

This is a minimal RMarkdown example to reproduce my problem.

---
title: "Knitr test"
date: "6 April 2015"
output: pdf_document
---


```{r, echo=FALSE, fig.width=6.5,fig.height=10}
library(ggplot2)
for (i in seq(1, 4)){
    p <- ggplot(cars, aes(speed, dist)) + geom_point() 
    print(p)
}
```

The generated pdf file looks like this. Two figures are printed in the page.

If I change the fig.height, add a few section in the rmd file, two figures are still printed in the same page with different arrangement.

---
title: "Knitr test"
output: pdf_document
date: "6 April 2015"
---

## Section A

Row B

```{r plot_phenotype, echo = FALSE, fig.height=8, fig.width=6.5}
library(ggplot2)
for (i in seq(1, 4))
{
    p <- ggplot(cars, aes(speed, dist)) + geom_point()
    print(p)
}

```

Thanks for any suggestion to fix this problem.

I am using RStudio 0.99.375. This is my session information.

sessionInfo()
R version 3.1.3 (2015-03-09)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

locale:
[1] LC_COLLATE=English_Australia.1252  LC_CTYPE=English_Australia.1252   
[3] LC_MONETARY=English_Australia.1252 LC_NUMERIC=C                      
[5] LC_TIME=English_Australia.1252    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] rmarkdown_0.5.3.1 knitr_1.9.5      

loaded via a namespace (and not attached):
 [1] colorspace_1.2-5 digest_0.6.8     evaluate_0.5.5   formatR_1.0     
 [5] ggplot2_1.0.0    grid_3.1.3       gtable_0.1.2     htmltools_0.2.6 
 [9] MASS_7.3-34      munsell_0.4.2    plyr_1.8.1       proto_0.3-10    
[13] Rcpp_0.11.5      reshape2_1.4.1   scales_0.2.4     stringr_0.6.2   
[17] tcltk_3.1.3      tools_3.1.3      yaml_2.1.13     

Answer 1

I have solved my problem.

In the generated tex file, there aren't new lines after each figure. This tex code us generated using rmd file above:

\includegraphics{test_files/figure-latex/plot_phenotype-1.pdf}
\includegraphics{test_files/figure-latex/plot_phenotype-2.pdf}
\includegraphics{test_files/figure-latex/plot_phenotype-3.pdf}
\includegraphics{test_files/figure-latex/plot_phenotype-4.pdf}

The solution is to add a new line after each cycle to print a figure.

cat('\r\n\r\n')

Not sure why I need two "\r\n" here. The generated tex file looks like:

\includegraphics{test_files/figure-latex/plot_phenotype-1.pdf}

\includegraphics{test_files/figure-latex/plot_phenotype-2.pdf}

\includegraphics{test_files/figure-latex/plot_phenotype-3.pdf}

\includegraphics{test_files/figure-latex/plot_phenotype-4.pdf}

This is the full example of my Rmd file

---
title: "Knitr test"
output:
  pdf_document:
    keep_tex: yes
date: "6 April 2015"
---

## Section A

Row B

```{r plot_phenotype, echo = FALSE, fig.height=8, fig.width=6.5}
library(ggplot2)
library(grid)
for (i in seq(1, 4))
{
    grid.newpage()
    p <- ggplot(cars, aes(speed, dist)) + geom_point()

    print(p)
    cat('\r\n\r\n')
}


```