Is there a way of make it so that knitr caches stuff so that last_plot() works properly? For example this document:
---
output: pdf_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE, cache = TRUE)
library(ggplot2)
```
```{r cars}
ggplot(mtcars, aes(hp, mpg)) +
geom_point()
```
The first value is `r last_plot()$data$mpg[1]`
The first time is generated, it will have one figure and the text "The first value is 21". But the second time, the last inline code will fail.
Related
My R Markdown files contain code to save PDF files e.g.
pdf(paste0("plots/filtering/", exp_name, "_umap.pdf"))
walk(list(p4, p5, p6, p7), print)
dev.off()
When I knit to HTML, I get the following printed as part of the HTML.
## quartz_off_screen
## 2
Is there a way to prevent this? I already have the knitr chunk options message and warning set to FALSE.
Best wishes,
Lucy
Wrap the the call to dev.off with invisible(...).
MWE
---
title: "Test"
output: html_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
library(ggplot2)
library(purrr)
```
## R Markdown
```{r}
p1 <- ggplot(mtcars, aes(mpg, disp)) + geom_point()
p2 <- ggplot(mtcars, aes(mpg, disp, color = factor(vs))) + geom_point()
```
```{r}
pdf("mtcars.pdf")
walk(list(p1, p2), print)
invisible(dev.off())
```
I want to add two images side by side in R markdown, but with some space between them.
How can I adjust the space between the images? Thank you!
{width=50%}
{width=50%}
One option could be using ggdraw() + draw_image from {cowplot}
---
title: "Untitled"
output: html_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
```{r side_by_side, fig.align='center'}
library(cowplot)
ggdraw() +
draw_image("test_logo.png", width = 0.4) +
draw_image("test_animal.jpg", width = 0.4, x = 0.5)
```
Which looks like
Another option could be making white border for the images using image_border from the {magick} package so that even if there is no actual space between them, white border will look like a space.
```{r another_option, warning=FALSE, message=FALSE}
library(magick)
img1 <- image_read("test_logo.png")
bordered_img1 <- image_border(img1, "white", "20x20")
img2 <- image_read("test_animal.jpg")
bordered_img2 <- image_border(img2, "white", "20x20")
image_write(bordered_img1, "img1.png")
image_write(bordered_img2, "img2.jpg")
```
```{r side_img, out.width="50%"}
knitr::include_graphics(c("img1.png", "img2.jpg"))
```
Which looks like,
How do I tell to knitr to use theme_classic if I export my Rmd notebook to PDF and use dark_theme_gray from ggdark package if I export my Rmd notebook to HTML?
Try this. (Sorry. I had no ggdark installed. So I just used theme_gray for HTML output). knitr provides helper functions to check for is_html_output or is_latex_output.
---
title: "test"
output:
pdf_document: default
html_document: default
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
# Plot
```{r}
library(ggplot2)
p <- ggplot(mtcars, aes(hp, mpg)) +
geom_point()
if (knitr::is_html_output()) {
p + theme_gray()
} else if (knitr::is_latex_output()) {
p + theme_classic()
}
```
Using R markdown with PDF output, I want to cite a figure into another figure caption. I also want to cite a BibTex reference in the caption. Any ideas? Here's an example of code:
---
title: "Untitled"
author: "me"
date: "today"
output:
pdf_document:
latex_engine: lualatex
number_sections: no
linestretch: 1.5
bibliography: input/Library.bib
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = FALSE, warning = FALSE, message = FALSE)
```
```{r}
df <- mtcars
library(ggplot2)
```
```{r, fig.cap="some stuff"}
ggplot(df, aes(cyl, mpg)) + geom_point()
```
```{r, fig.cap="some more stuff. here I'd like to cite figure 1. I would also like a BibTex citation"}
ggplot(df, aes(cyl, hp)) + geom_point()
```
In my experience cross-referencing works better when one uses bookdown::pdf_document2 or bookdown::html_document2. Note that it makes sense to name the chunk that produces the figure since that name is used in the label used for referencing:
---
title: "Untitled"
author: "me"
date: "today"
output:
bookdown::pdf_document2:
latex_engine: lualatex
number_sections: no
bookdown::html_document2:
default
linestretch: 1.5
bibliography: packages.bib
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = FALSE, warning = FALSE, message = FALSE)
knitr::write_bib(c(.packages()), 'packages.bib')
```
```{r}
df <- mtcars
library(ggplot2)
```
```{r stuff, fig.cap="some stuff"}
ggplot(df, aes(cyl, mpg)) + geom_point()
```
```{r, fig.cap="some more stuff. here I'd like to cite figure \\#ref(fig:stuff). I would also like a BibTex citation [#R-base]"}
ggplot(df, aes(cyl, hp)) + geom_point()
```
For the BibTeX reference I am using an automatically created one, but the adaption to your case should be obvious.
I recently started using xaringan and it's really neat. Thanks Yihui for the great package. One question I was wondering, is it possible to programmatically generate slides, each containing a plotly plot, in a for loop? I know I can generate slides of ggplots like this, where ggplot_list is a list of ggplots:
```{r, message=FALSE, warning=FALSE, results='asis'}
for (p in ggplot_list) {
cat("\n\n---\n")
print(p)
}
```
This works perfectly.
I can also include individual plotly plots by calling ggplotly(ggplot_list[[1]]), which also works perfectly.
But I can't seem to get the combination of the two to work, naively doing the following generates empty slides for me.
```{r, message=FALSE, warning=FALSE, results='asis'}
for (p in ggplot_list) {
cat("\n\n---\n")
ggplotly(p)
}
```
Update: here I include a minimal example of things I've tried so far.
---
title: "xaringan + plotly + loop?"
subtitle: "Does it work?"
author: "Fenfen Kan"
date: "2017/13/32"
output:
xaringan::moon_reader:
lib_dir: libs
nature:
highlightStyle: github
highlightLines: true
countIncrementalSlides: false
---
```{r setup, include=FALSE}
options(htmltools.dir.version = FALSE)
```
# Several boring ggplots
```{r, message=FALSE, warning=FALSE}
library(ggplot2)
library(plotly)
p1 <- ggplot(iris, aes(Sepal.Length, Sepal.Width)) +
geom_point(aes(color=Species))
p2 <- ggplot(iris, aes(Petal.Length, Petal.Width)) +
geom_point(aes(color=Species))
p3 <- ggplot(iris, aes(Sepal.Length, Petal.Length)) +
geom_point(aes(color=Species))
ggplot_list <- list(p1, p2, p3)
```
---
# Invididual plotly works
```{r}
ggplotly(p1)
```
---
# ggplot slides in loop also works
```{r, message=FALSE, warning=FALSE, results='asis'}
for (p in ggplot_list) {
cat("\n\n---\n")
print(p)
}
```
---
# plotly in loop doesn't work
```{r, message=FALSE, warning=FALSE, results='asis'}
for (p in ggplot_list) {
cat("\n\n---\n")
ggplotly(p)
}
```
# print(ggplotly(p)) in loop doesn't work either
```{r, message=FALSE, warning=FALSE, results='asis'}
for (p in ggplot_list) {
cat("\n\n---\n")
print(ggplotly(p))
}
```
I figured out a solution when trying to do a similar thing in knitr recently. I added it to the above example. See the last section - It generates 3 plotly slides in a loop.
---
title: "xaringan + plotly + loop?"
subtitle: "Does it work?"
author: "Fenfen Kan"
date: "2017/13/32"
output:
xaringan::moon_reader:
lib_dir: libs
nature:
highlightStyle: github
highlightLines: true
countIncrementalSlides: false
---
```{r setup, include=FALSE}
options(htmltools.dir.version = FALSE)
```
# Several boring ggplots
```{r, message=FALSE, warning=FALSE}
library(ggplot2)
library(plotly)
library(knitr)
p1 <- ggplot(iris, aes(Sepal.Length, Sepal.Width)) +
geom_point(aes(color=Species))
p2 <- ggplot(iris, aes(Petal.Length, Petal.Width)) +
geom_point(aes(color=Species))
p3 <- ggplot(iris, aes(Sepal.Length, Petal.Length)) +
geom_point(aes(color=Species))
ggplot_list <- list("p1"=p1, "p2"=p2, "p3"=p3)
```
---
# Invididual plotly works
```{r}
ggplotly(p1)
```
---
# ggplot slides in loop also works
```{r, message=FALSE, warning=FALSE, results='asis'}
for (p in ggplot_list) {
cat("\n\n---\n")
print(p)
}
```
---
# plotly in loop doesn't work
```{r, message=FALSE, warning=FALSE, results='asis'}
for (p in ggplot_list) {
cat("\n\n---\n")
ggplotly(p)
}
```
# print(ggplotly(p)) in loop doesn't work either
```{r, message=FALSE, warning=FALSE, results='asis'}
for (p in ggplot_list) {
cat("\n\n---\n")
print(ggplotly(p))
}
```
# generate chunks, then explicitly calling `knit` works!
```{r create-markdown-chunks-dynamically, include=FALSE}
out = NULL
for (p_name in names(ggplot_list)) {
knit_expanded <- paste0("\n\n---\n## Plot: ", p_name, "\n\n```{r results='asis', echo=FALSE, warning=FALSE, message=FALSE}\n\nggplotly(ggplot_list[['", p_name, "']])\n\n```")
out = c(out, knit_expanded)
}
```
<!--- knit those table chunk statements -->
`r paste(knit(text = out), collapse = '\n')`