如何将（多页）pdf添加到rmarkdown？

Question

考虑这个简单的例子

library(dplyr)
library(ggplot2)
library(tidyr)

mydata <- data_frame(group = c('a', 'a', 'a', 'b', 'b', 'b'),
                     x = c(1,2,3,5,6,7),
                     y = c(3,5,6,4,3,2))

mydata2 <- mydata %>% group_by(group) %>% 
  nest() %>% 
  mutate(myplot = map(data, ~ggplot(data = .x, aes(x = x, y = x)) + geom_point()))

pdf("P://mychart.pdf")
print(mydata2$myplot)
dev.off()

上面的代码将输出一个有两页的pdf。如何在我的rmarkdown 文档中显示这两页？

使用

---
title: "crazy test"
output:
  pdf_document
---

```{r global_options, include=FALSE}
knitr::opts_chunk$set(echo = TRUE, fig.pos = 'h')
```


ttt

## this is a test!!

```{r label, out.width = "85%", fig.cap = "caption"}
knitr::include_graphics(path = "P://mychart.pdf")
```

只会显示pdf的首页！另一个图表在哪里？ :(

有什么想法吗？

谢谢！

Answer 1

可以使用pdfpages 一次包含PDF 文件中的多个页面。但是，这些都包含在单独的页面上。虽然可以添加页码，但您不能轻松地将这些图像放入figure 环境中。幸运的是，\includegraphics 可以选择使用 PDF 中的单个页面。不幸的是，knitr::include_graphics 不允许将其他参数传递给\includegraphics。

这两种可能性：

---
title: "crazy test"
output:
  pdf_document
header-includes:
  - \usepackage{pdfpages}
---

```{r global_options, include=FALSE}
knitr::opts_chunk$set(echo = TRUE, fig.pos = 'h')
```


```{r, include=FALSE}
library(dplyr)
library(ggplot2)
library(tidyr)
library(purrr)

mydata <- data_frame(group = c('a', 'a', 'a', 'b', 'b', 'b'),
                     x = c(1,2,3,5,6,7),
                     y = c(3,5,6,4,3,2))

mydata2 <- mydata %>% group_by(group) %>% 
  nest() %>% 
  mutate(myplot = map(data, ~ggplot(data = .x, aes(x = x, y = x)) + geom_point()))

pdf("mychart.pdf")
print(mydata2$myplot)
dev.off()
```


## this is a test!!

Only first page

```{r label, out.width = "85%", fig.cap = "caption"}
knitr::include_graphics(path = "mychart.pdf")
```

All pages but w/o caption and taking a full page

\includepdf[pages=-,nup=2,pagecommand={}]{mychart.pdf}

Alternative, using explicit LaTeX commands.

\begin{figure}
\includegraphics[page=1,width=0.5\linewidth]{mychart.pdf}
\includegraphics[page=2,width=0.5\linewidth]{mychart.pdf}
\caption{\label{fig:test} Test.}
\end{figure}

也可以将它们放入带有cat() 和result = 'asis' 的R 块中。但是，设置标题等选项仍然没有使用。

Answer 2

这是带有 staplr 的 Rmd 解决方案。请注意，您需要安装 pdftk 才能使 split_pdf 工作

---
title: "crazy test"
output:
  pdf_document
---

```{r global_options, include=FALSE}
knitr::opts_chunk$set(echo = TRUE, fig.pos = 'h')
```

## Split pdf

```{r}
staplr::split_pdf("mychart.pdf", output_directory = ".", prefix = "mychart_")
```

## Add pdfs

```{r label, out.width = "85%", fig.cap = c("caption 1", "caption 2"), echo = FALSE}
flist <- list.files()
mychart_files <- flist[grep("mychart_", flist)]
knitr::include_graphics(mychart_files)
```

另外，包含图形不能循环工作。但它接受多个路径，所以效果很好。

Answer 3

knitr 有一个名为out.extra 的特定块选项，允许将选项传递给\includegraphics 命令。在knitr doc 中查看此选项。

这意味着它可以用于分页选项page。使用上面的例子，你可以这样做

---
title: "crazy test"
output:
  pdf_document:
    keep_tex: TRUE
---

```{r global_options, include=FALSE}
knitr::opts_chunk$set(echo = TRUE, fig.pos = 'h')
```


```{r, include=FALSE}
library(dplyr)
library(ggplot2)
library(tidyr)
library(purrr)

mydata <- tibble(group = c('a', 'a', 'a', 'b', 'b', 'b'),
                     x = c(1,2,3,5,6,7),
                     y = c(3,5,6,4,3,2))

mydata2 <- mydata %>% group_by(group) %>% 
  nest() %>% 
  mutate(myplot = map(data, ~ggplot(data = .x, aes(x = x, y = x)) + geom_point()))

pdf("mychart.pdf")
print(mydata2$myplot)
dev.off()
```

Only first page

```{r label, out.width = "85%", fig.cap = "caption"}
knitr::include_graphics(path = "mychart.pdf")
```

second page

```{r label2, out.width = "85%", fig.cap = "caption", out.extra="page=2"}
knitr::include_graphics(path = "mychart.pdf")
```