knitr + pandoc: cannot see plot when viewing html slides

StackOverflow https://stackoverflow.com/questions/20362835

  •  28-08-2022
  •  | 
  •  

Вопрос

I have successfully created 2 tests slides in R Studio using the knitr package and pandoc. The R markdown file when using the "knitr" button in R studio looks fine and shows plots correctly, however when using pandoc to generate a .html file from the .Rmd file, running in the browser seems to lose all code wrapping and plots from the Rmd file. Here are my two scripts:

mdown.Rmd:

Title
========================================================

This is an R Markdown document. Markdown is a simple formatting syntax for authoring web pages (click the **MD** toolbar button for help on Markdown).

When you click the **Knit HTML** button a web page will be generated that includes both content as well as the output of any embedded R code chunks within the document. You can embed an R code chunk like this:

```{r}
summary(cars)
```

---

You can also embed plots, for example:

```{r fig.width=7, fig.height=6}
plot(cars)
```

and the script to run it:

# Load packages
setwd("~Documents")
require(knitr)
require(markdown)

# Create slides
knit('mdown.Rmd')
system('pandoc -s -t slidy mdown.Rmd -o mdown.html')

also here is the html file generated by pandoc

<?xml version="1.0" encoding="utf-8"?>
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
 "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"> 
<head>
  <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
  <meta name="generator" content="pandoc" />
  <link rel="stylesheet" type="text/css" media="screen, projection, print" 
    href="http://www.w3.org/Talks/Tools/Slidy/slidy.css" /> 
  <script src="http://www.w3.org/Talks/Tools/Slidy/slidy.js.gz"
    charset="utf-8" type="text/javascript"></script>
</head>
<body>
<div class="slide">

<h1>Title</h1>
<p>This is an R Markdown document. Markdown is a simple formatting syntax for authoring web pages (click the <strong>MD</strong> toolbar button for help on Markdown).</p>
<p>When you click the <strong>Knit HTML</strong> button a web page will be generated that includes both content as well as the output of any embedded R code chunks within the document. You can embed an R code chunk like this:</p>
<p><code>{r} summary(cars)</code></p>
</div>

<div class="slide">

<p>You can also embed plots, for example:</p>
<p><code>{r fig.width=7, fig.height=6} plot(cars)</code></p>
</div>
</body>
</html>

where am I going wrong here?

Это было полезно?

Решение

You are processing the .Rmd file with pandoc where you should be processing the .md file created after running mdown.Rmd through knitr.

knit('mdown.Rmd')
system('pandoc -s -t slidy mdown.md -o mdown.html')

The .Rmd file is simply the original file you showed above.

Лицензировано под: CC-BY-SA с атрибуция
Не связан с StackOverflow
scroll top