I am using RMarkdown to create a html file (my preferred format). I then use the officer package to create a powerpoint (PPT) (everyone else's preferred format) that reads in the .png images that are automatically created and saved when I knit the document (I believe this is default when the fig.path is specified).
To get consistent fontsize throughout the PPT figures, I have specified in each knitr chunk fig.width, out.width, etc to be equal to the relevant PPT placeholder dimensions. E.G if the PPT placeholder is 5.29in high x 5.89in wide, then in the knitr chunk I specify , out.height="5.29in", out.width="5.89in", fig.height=5.29, fig.width=5.89). This seems to work in terms of the PPT file, however it results in extremely small figures for the HTML file. Is there a way to get the knitr code to work for both html and PPT, without needing to specifically save the image, using, for example ggsave()?
Following is some auto-generated test code:
---
title: "Test_Figure_Size"
output:
html_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(fig.path = "Delete_Me/", echo=FALSE)
```
When you include out.height, out.width the figure is extremely small in the knitted html document, but perfectly sized as a .png file.
```{r pressure, echo=FALSE, out.height="5.29in", out.width="5.89in", fig.height=5.29, fig.width=5.89}
plot(pressure)
```
When you say out.height="5.29in", out.width="5.89in", those values are written into the HTML output as height and width attributes of the img. But height and width are expressed in pixels, so you'll end up with a figure about 5 pixels square.
I don't use Powerpoint, but is there a way to specify the image size in pixels, e.g. "589px" or something similar? Then it will use the same scale as the browser, and things should be consistent.
Related
I'm trying to create a summary table with the package vtable. I do get a table but somehow the font size is super large and not the whole table is shown? I'm really at a loss here. I have spent hours on it, but could not find a solution... Can please someone tell me how to get a smaller table (font size and the whole table in a pdf document?
---
title: "Example"
date: "22 March 2021"
output:
pdf_document
---
{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
library(vegan)
library(vtable)
{r dune}
data(dune.env)
{r plot1, echo = F,results='asis',out.width='10%',message=F, fig.show='hold'}
st(dune.env,summ=c('mean(x)','median(x)','min(x)','max(x)'),group="Management",group.long = TRUE,out="latex")
By default, sumtable with out = 'latex' applies a LaTeX \resizebox{\textwidth} to the table to make it fit horizontally on the page. When the table is very narrow and tall, though, like this one, the resizebox can scale it to be bigger (making the text big).
You can control the width of the table with the fit.page option, which scales the horizontal width of the table. By default it's '\\textwidth', but you could do, for example, .6\\textwidth to only fill 60% of the horizontal space. This is what I get with fit.page='.5\\textwidth':
Now, this makes the text tiny, but it does fit. This is a consequence of LaTeX giving tall tables a hard time, and having no built-in support for multi-page tables. So it just fills up a page and the rest isn't shown. This is a LaTeX thing, not sumtable. There isn't currently support for multi-page LaTeX tables in sumtable/vtable. However, you could add keep_tex: true to your YAML, then after the fact go in and edit the TeX file to use the longtable LaTeX package, which adds support for multi-page tables, and turn the \begin{table} into \begin{longtable}, etc..
I'm using Rmarkdown to create pdf files. I have chunks inside the .Rmd file like this one:
```{r}
knitr::include_graphics('image.png')
```
This is converted in the .tex file to:
\begin{Shaded}
\begin{Highlighting}[]
\NormalTok{knitr}\OperatorTok{::}\KeywordTok{include_graphics}\NormalTok{(}\StringTok{'image.png'}\NormalTok{)}
\end{Highlighting}
\end{Shaded}
\includegraphics[width=8.88in]{image}
Unfortunately, in most cases that I've seen the width is not appropriate. How to automatically remove the "[width=8.88in]" ? On an other computer the width was not set like this, even with the same .Rmd file, and the images had the appropriate size.
But I cannot figure where this difference comes from, as I do not have access to this computer anymore.
Thank you
Please see the argument dpi on the help page ?knitr::include_graphics. In short:
knitr::include_graphics('image.png', dpi = NA)
Or manually specify a width via the out.width chunk option.
I'm trying to build an automated report that will have three charts right underneath each other without margin space between each other.
I've mocked up my problem with the following Rmd script
---
output: pdf_document
---
```{r setup, include=FALSE}
library(gridExtra)
```
```{r, echo=FALSE}
car_tbl <- tableGrob(mtcars[1:10,])
grid.arrange(car_tbl, car_tbl, car_tbl)
```
You can see how the tables overlap each other. There seems like there are actually a few issues comprising my problem.
How do I use the options of tableGrob and grid.arrange to keep the tables from overlapping.
How do I make sure nothing is cut off? In other words, how do I set the graphic to take the whole page if I need it too?
How can I re-actively shrink the text of the plot to fit on one page?
How can I set the size of the page to whatever size I want? Are there options set the knitr document to print to a pdf page of any size I want? Perhaps poster size if I need it to?
There are different angles to approach your question. Here's a working example with three tables fitting in one chunk placed on a pdf of size A2.
---
output: pdf_document
geometry: paper=a2paper
---
```{r setup, include=FALSE}
library(gridExtra)
```
```{r, echo=FALSE, fig.height=10}
car_tbl <- tableGrob(mtcars[1:10,])
grid.arrange(car_tbl, car_tbl, car_tbl)
```
To address your questions specifically,
1. How do I use the options of tableGrob and grid.arrange to keep the tables from overlapping.
Their overlap had more to do with the default fig.height set by knitr.
2. How do I make sure nothing is cut off? In other words, how do I set the graphic to take the whole page if I need it too?
Make sure the figure height and page are big enough for the table.
3. How can I re-actively shrink the text of the plot to fit on one page?
It's not trivial, but I guess it could be done. I doubt it's a good idea though (for typographical reasons): typically the font size should be set, and if the table doesn't fit, it should be split into several pages (there's an example in a link I provided).
3. How can I set the size of the page to whatever size I want? Are there options set the knitr document to print to a pdf page of any size I want? Perhaps poster size if I need it to?
It's a latex question, which in the context of Rmd documents means that you could pass these layout options to latex via rmarkdown and pandoc, typically as options for the geometry package.
I'm producing a solutions manual for a book, using .Rmd files with the following YAML header:
---
title: "DDAR: Solutions and Hints for Exercises"
date: "`r Sys.Date()`"
output:
word_document:
reference_docx: solutions-setup.docx
---
where I control the general layout of the document with the reference_docx to get an output Word document.
There will be many figures, and I'd like to set some global graphics parameters to give relatively tight bounding boxes and reasonable font sizes
in the figures without having to tweak each one from what I see in a PDF document.
I tried the following, but the par() setting doesn't seem to have any effect:
{r setup, echo=FALSE}
options(digits=4)
par(mar=c(5,4,1,1)+.1)
Instead I get images like the following in my document with larger bounding boxes than I would like and with much larger font sizes than I would like.
I know how to control all this in .Rnw files produced with LaTeX, but I
can't find how to do it in .Rmd -> Word. Is there a chunk hook I could
use? I don't think that there is an out.width chunk option that re-scales
a figure as in LaTeX.
#scoa's answer shows how to use a hook to set some graphical parameters at the beginning of each chunk. This is necessary because "by default, knitr opens a new graphics device to record plots and close it after evaluating the code, so par() settings will be discarded", i.e. graphical parameters for later chunks cannot be set in an early setup-chunk but need to be set for each chunk separately.
If this behavior is not wanted, the package option global.par = TRUE can be used:
opts_knit$set(global.par = TRUE)
Finding the correct values for the margins is sometimes quite painful. In these cases, hook_pdfcrop can help. In all chunks where the option crop = TRUE, white margins will be removed. To apply this to all chunks, use
library(knitr)
knit_hooks$set(crop = hook_pdfcrop)
opts_chunk$set(crop = TRUE)
This works for docx output as well because "when the plot format is not PDF (e.g. PNG), the program convert in ImageMagick is used to trim the white margins" (from ?hook_pdfcrop).
Note that under some circumstances, cropping plots has the side effect of sometimes apparently different "zoom" factors of plots: This happens in cases where we start with identical sized elements on two plots but larger white margins around one of the plots. If then both are resized to a fixed output width after cropping, elements on the plot with larger margins look larger. However, this is not relevant for docx output because out.width/out.height cannot be used in that case.
The knitr documentation for hooks actually uses small margins as an example of what you can do with hooks. Here is a solution (adapted from this documentation).
---
output: word_document
---
```{r setup, echo=FALSE}
library(knitr)
knit_hooks$set(small.mar = function(before, options, envir) {
if (before) par(mar=c(5,4,1,1)+.1) # smaller margin on top and right
})
opts_chunk$set(small.mar=TRUE)
```
```{r}
plot(iris$Sepal.Length)
```
Using opts_chunk$set(small.mar=TRUE) is a way to avoid passing it to every chunk in the document.
The margin appears fixed (screenshot from the docx output in libreoffice with default reference-docx).
I'm using Rmarkdownv2 to generate a pdf file with some local images. But it seems that the image was converted to a larger size with lower resolution in the rendered pdf, compared to the html. The code I'm currently using for the image is something like:
Is there any way to control the image size in the pdf? I also tried
pdf_document:
fig_height: 1
fig_width: 2
But that didn't work. Thanks in advance.
You can use the development version of knitr (>= v1.11.22) and the include_graphics() function, e.g.
```{r out.width='70%'}
knitr::include_graphics('figures/fig1.png')
```
If you want a figure caption, just use the chunk option fig.cap = 'A figure caption.'