I would like to adjust the row padding in a jtools regression table. I tried set_row_height since I read that the underlying structure is a huxtable. But I'm unsure, and it didn't work.
---
title: "Untitled"
author: "Name"
date: "10 5 2021"
output: html_document
---
## R Markdown
```{r, warning=FALSE, message=FALSE}
mymodel <- lm(mpg ~ ., data=mtcars)
library(tidyverse)
library(jtools)
library(huxtable)
export_summs(mymodel, scale = TRUE) %>%
set_font_size(6) %>% # working in markdown html
set_row_height(., everywhere, 0.1) # not working in html
```
It looks fine in RStudio, but uses extensive row space in Markdown. set_font_size is working, but set_row_height not.
Finally, row height adjustment worked with set_tb_padding. I cannot replicate why it didn't worked in the first place. set_row_height requires CSS/LaTeX values, i.e. set_row_height("4cm"). I cannot reduce row height to a resonable size but can increase row height.
title: "Jtools and Huxtable"
author: "Name"
date: "10 5 2021"
output: html_document
---
## R Markdown
```{r, warning=FALSE, message=FALSE}
mymodel <- lm(mpg ~ ., data=mtcars)
library(tidyverse)
library(jtools)
library(huxtable)
export_summs(mymodel, scale = TRUE) %>%
set_font_size(10) %>%
set_tb_padding(1)
```
Related
I have a list of 300 plots and want one PowerPoint slide to show one plot (300 slides). What's the best way to achieve this?
A toy example using the built-in iris dataset to create a list of plots:
purrr::map(names(iris[,-5]), function(col_name){
plot = iris %>%
ggplot(aes(x = !!as.name(col_name))) +
geom_histogram()
return(plot)
})
I hope to create PowerPoint slides with one plot on each slide.
I will be using the iris data set, which is a built-in data set often used to populate example code.
With the following code in a Rmd file:
---
title: "Test_PowerPoint"
author: "KoenV"
date: '2022-06-30'
output: powerpoint_presentation
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = FALSE)
```
```{r include=FALSE, warning=FALSE, message=FALSE}
library(tidyverse)
library(purrr)
```
```{r, iris, fig.cap="A scatterplot.", echo=FALSE, warning=FALSE, message=FALSE}
## your code
purrr::map(names(iris[,-5]), function(col_name){
plot = iris %>%
ggplot(aes(x = !!as.name(col_name))) +
geom_histogram()
return(plot)
})
```
And after hitting the "knit" button, you will see a PowerPoint presentation appearing, with the following lay-out:
Please let me know, whether this is what you wanted.
I need to implement a figure caption in a plot that is generated by the vtree package in R markdown. I learned that this is a htmlwidget and figure captions should now be possible for htmlwidgets used in R markdown with install.packages('webshot') and webshot::install_phantomjs() (reference: https://bookdown.org/yihui/bookdown/html-widgets.html#ref-R-DT.
But days after I am not really any step further. I did not find any example (show case) for this issue (fig.cap for htmlwidgets in R markdown in the net) so my hope is that someone out there can give me some help!
In my iris dataset example, in Fig. 1 the caption is not working in contrast to Fig. 2.
my iris set example RMD file:
YAML
---
title: "test"
author: "TJ"
date: "14 12 2020"
output: html_document
---
code chunk 1: load libraries and data
knitr::opts_chunk$set(echo = TRUE)
library(vtree)
library(webshot)
library(tidyverse)
attach(iris)
df <- iris %>%
select(Species) %>%
cbind(sapply(levels(.$Species), `==`, .$Species))
code chunk 2: Figure 1
{r fig1, echo=FALSE, fig.cap="Vtree plot"}
vtree(iris, "Species")
code chunk 3: Figure 2
{r fig2, echo=FALSE, fig.cap="Scatter plot iris dataset"}
plot(Sepal.Length, Sepal.Width, main="Scatterplot Example",
xlab="Sepal Length ", ylab="Sepal Width ", pch=19)
There is a workaround using the Magick package.You save the image as .png using grVizToPNG (make sure you comment this line out before you render your document or put it in a separate chunk with ยด{r eval = FALSE}, otherwise you will get an error during rendering:
```{r eval=FALSE, echo = FALSE}
myimage <- vtree(iris, "Species")
saveMyimage <- grVizToPNG(myimage, width=800)
```
Here you use the Magickpackage:
```{r magick, echo= FALSE}
MyimagePNG <- image_read("myimage.png")
image_annotate(MyimagePNG, "Vtree plot", size = 35, gravity = "southwest")
```
Cross-referencing a table made by texreg in bookdown halfway works. The table is numbered properly but the cross-reference ends up as '??' in the text. A MRE is below. Is there a solution to this, or is there another package that can solve this problem (stargazer has the same problem in bookdown). Using fig.cap has no effect.
Thanks for any help.
---
title: "bookdownTest"
author: "Richard Sherman"
date: "1/9/2020"
output:
bookdown::pdf_document2:
fig_caption: yes
toc: false
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
```{r load libraries, include=FALSE}
library(texreg)
library(bookdown)
```
```{r lm, results='asis', star.symbol = "\\*", center = TRUE}
m1 <- lm(mpg ~ disp + cyl + hp, mtcars)
m2 <- lm(mpg ~ disp + hp, mtcars)
texreg(list(m1, m2), center = TRUE,
caption="Linear model of mpg")
```
Results are in Table \#ref(tab:lm).
texreg() has a label option that lets you set the label, so you can do:
texreg(list(m1, m2), center = TRUE,
caption="Linear model of mpg",
label="tab:lm")
You may have been relying on the automatic table labels described in the bookdown documentation, but that only works when using the knitr::kable() function to generate your table.
The following knitr code give me the plot below -- how do I plot it in a landscape orientation?
```{r}
rm(list=ls())
library(tree)
set.seed(1111)
x1<-runif(100)
x2<-rnorm(100,mean=.3)
x3<-runif(100)
d1<-x1>0.5
d2<-x2>0.7
d3<-x3<0.2
y<-ifelse(d1,1,ifelse(d2,2,ifelse(d3,3,4)))
df<-data.frame(x1,x2,x3,y)
tr<-tree(y~.,data=df)
plot(tr)
text(tr)
```
If your want a pdf/LaTeX output it is quite easy with out.extra='angle=90' chunk argument :
---
title: "Rotation test"
output: pdf_document
---
```{r, out.extra='angle=90'}
rm(list=ls())
library(tree)
set.seed(1111)
x1<-runif(100)
x2<-rnorm(100,mean=.3)
x3<-runif(100)
d1<-x1>0.5
d2<-x2>0.7
d3<-x3<0.2
y<-ifelse(d1,1,ifelse(d2,2,ifelse(d3,3,4)))
df<-data.frame(x1,x2,x3,y)
tr<-tree(y~.,data=df)
plot(tr)
text(tr)
```
In some circumnstances it is better to keep the graph as it but to rotate just one page in landscape format within you document.
You need pdflscape LaTeX package for this (included for example in the texlive-latex-base package in Ubuntu as "oberdiek").
In the following example the graph is extended to occupy a full A4 page in landscape format. NB : you must specify fig.align='center' to make it work.
---
title: "Rotation test"
output: pdf_document
header-includes:
- \usepackage{pdflscape}
---
```{r}
rm(list=ls())
library(tree)
set.seed(1111)
x1<-runif(100)
x2<-rnorm(100,mean=.3)
x3<-runif(100)
d1<-x1>0.5
d2<-x2>0.7
d3<-x3<0.2
y<-ifelse(d1,1,ifelse(d2,2,ifelse(d3,3,4)))
df<-data.frame(x1,x2,x3,y)
tr<-tree(y~.,data=df)
```
\newpage
\begin{landscape}
```{r fig.align='center', fig.width = 27/2.54, fig.height = 19/2.54}
plot(tr)
text(tr)
```
\end{landscape}
```{r}
summary(tr)
```
I am creating a series of plots from within a loop in an RMarkdown document, then knitting this to a PDF. I can do this without any problem, but I would like the caption to reflect the change between each plot. A MWE is shown below:
---
title: "Caption loop"
output: pdf_document
---
```{r, echo=FALSE}
library(tidyverse)
p <-
map(names(mtcars), ~ggplot(mtcars) +
geom_point(aes_string(x = 'mpg', y = .))) %>%
set_names(names(mtcars))
```
```{r loops, fig.cap=paste(for(i in seq_along(p)) print(names(p)[[i]])), echo=FALSE}
for(i in seq_along(p)) p[[i]] %>% print
```
I have made a first attempt at capturing the plots and storing in a variable p, and trying to use that to generate the captions, but this isn't working. I haven't found too much about this on SO, despite this surely being something many people would need to do. I did find this question, but it looks so complicated that I was wondering if there is a clear and simple solution that I am missing.
I wondered if it has something to do with eval.after, as with this question, but that does not involve plots generated within a loop.
many thanks for your help!
It seems that knitr is smart enough to do the task automatically. By adding names(mtcars) to the figure caption, knitr iterates through these in turn to produce the correct caption. The only problem now is how to stop all of the list indexes from printing in the document...
---
title: "Caption loop"
output: pdf_document
---
```{r loops, fig.cap=paste("Graph of mpg vs.", names(mtcars)), message=FALSE, echo=FALSE, warning=FALSE}
library(tidyverse)
map(
names(mtcars),
~ ggplot(mtcars) +
geom_point(aes_string(x = 'mpg', y = .))
)
```
In case this might be useful to somebody. Here is an adaptation of Jonny's solution for captions without printing list indices. This can be achieved by using purrr::walk instead of purrr::map. Also included is a latex fig label and text that references each plot.
---
title: "Loop figures with captions"
output:
pdf_document
---
```{r loops, fig.cap=paste(sprintf("\\label{%s}", names(mtcars)), "Graph of mpg vs.", names(mtcars)),results='asis', message=FALSE, echo=FALSE, warning=FALSE}
library(tidyverse)
library(stringi)
walk(names(mtcars),
~{
p <- ggplot(mtcars) +
geom_point(aes_string(x = 'mpg', y = .))
#print plot
cat('\n\n')
print(p)
#print text with refernce to plot
cat('\n\n')
cat(sprintf("Figure \\ref{%s} is a Graph of mpg vs. %s. %s \n\n", ., .,
stri_rand_lipsum(1)))
cat("\\clearpage")
})
```