r markdown output to pdf: stop plot breaking up a code chunk - r

Question

I am printing an r markdown file to pdf. I've tried various output specifications, but the plot keeps displaying in the middle of segments [1] and [2].
I want the all of the code to be displayed one chunk, and will call the plot later in the document.
```{r, include=TRUE, results='hide'}
# [1] There is code up here
# [plot interrupts the code chunk here] Scatter plot
plot1 = plot(df$var1, df$var)
# [2] More code below this point
```

Answer 1

Use the chunk option fig.show = 'hold' to display all the plots produced by a chunk at the end of the chunk. Here is an example .Rmd file and output.
---
title: Stop Plot Breakikng Up Code Chunk
output: pdf_document
---
The key is to use the chunk option `fig.show = 'hold'` so that all plots from
the chunk will will displayed at the end of the chunk.
```{r setup, include = FALSE, cache = FALSE}
library(knitr)
opts_chunk$set(fig.show = "hold")
```
We'll use the `mtcars` data set for the example.
```{r plot1, include = TRUE, results = "hide"}
mean(mtcars$wt)
mean(mtcars$mpg)
plot(mtcars$wt, mtcars$mpg)
var(mtcars$wt)
```
End of example.
EDIT:
Another solution, closer to what I think you are looking for, is to use ref.label to reuse code chunks.
---
title: Stop Plot Breaking Up Code Chunk
output: pdf_document
---
The key is to use the chunk option `fig.show = 'hold'` so that all plots from
the chunk will will displayed at the end of the chunk.
```{r setup, include = FALSE, cache = FALSE}
library(knitr)
opts_chunk$set(fig.show = "hold",
collapse = TRUE)
```
We will use the `mtcars` data set for the example.
```{r all_code}
```{r mean_code, ref.label = "means", echo = TRUE, results = "hide"}
```{r plot1_code, ref.label = "plot1", echo = TRUE, fig.show = "hide", fig.keep = "none"}
```{r var_code, ref.label = "var_wt", echo = TRUE, results = "hide"}
```
Description of a plot
```{r "plot1", echo = FALSE}
plot(mtcars$wt, mtcars$mpg)
```
More text.
Below here, chunks that are evaluated, but not shown.
```{r means, include = FALSE}
mean(mtcars$wt)
mean(mtcars$mpg)
```
```{r var_wt, include = FALSE}
var(mtcars$wt)
```
End of the example.

Answer 2

You can write 2 chunks :
## Title
Herebelow the code are not separated by plots :
```{r display_code_only, eval=FALSE}
plot(pressure)
plot(iris)
```
Herebelow the plot are not separated by code :
```{r display_plot_only, echo=FALSE}
plot(pressure)
plot(iris)
```