I recently tried using officedown to create a .docx report of my document. In my documents I import images from an \images folder in my project directory.
Normally when I knit a document I am able to maximize its position on the page.
Does anyone know how to do this using officedown? I have no issues when I run this code in RMarkdown
This is what I get using officedown
This is what I want (notice the image is taking up the whole page)
I have included a reprex below
---
date: "`r Sys.Date()`"
author:
title: "GitHub Example"
output:
officedown::rdocx_document
---
```{r setup, include=FALSE, echo = FALSE}
pacman::p_load(readxl, dplyr, apastats, officedown, officer, ggplot2, knitr) # load packages
knitr::opts_chunk$set(fig.align = 'center',
fig.cap = TRUE,
fig.pos = 'H',
fig.path = 'images/',
echo = FALSE,
warning = FALSE,
message = FALSE,
include = TRUE,
out.height="100%", out.width="100%",
dpi = 300)
```
```{r}
# Creating a boxplot and saving it in \images directory
plot <- ggplot(iris, aes(x = Sepal.Length, y = Sepal.Width, color = Species)) +
geom_boxplot()
ggsave("images/plot.png",plot, width=11, height=8.5, dpi=300)
```
## Figures
Figure \#ref(fig:boxplot) shows a boxplot that is made within the RMarkdown document.
I want to call in an image saved from a previous R scripts which is saved
in my `\images` directory shown in Figure \#ref(fig:plot). But notice how it
does not take up the whole page.
<!---BLOCK_LANDSCAPE_START--->
```{r fig.cap="A boxplot", fig.id = "boxplot"}
ggplot(iris, aes(x = Sepal.Length, y = Sepal.Width, color = Species)) +
geom_boxplot()
```
<!---BLOCK_LANDSCAPE_STOP--->
<!---BLOCK_LANDSCAPE_START--->
```{r fig.id="plot", fig.cap="boxplot imported from images folder", echo=FALSE}
knitr::include_graphics("images/plot.png")
```
<!---BLOCK_LANDSCAPE_STOP--->
You can use knitr usual parameters fig.width and fig.height (inches).
---
date: "`r Sys.Date()`"
author:
title: "GitHub Example"
output:
officedown::rdocx_document
---
```{r setup, include=FALSE, echo = FALSE}
pacman::p_load(readxl, dplyr, apastats, officedown, officer, ggplot2, knitr) # load packages
knitr::opts_chunk$set(fig.align = 'center',
echo = FALSE,
warning = FALSE,
message = FALSE,
dpi = 300)
```
```{r}
plot <- ggplot(iris, aes(x = Sepal.Length, y = Sepal.Width, color = Species)) +
geom_boxplot()
```
<!---BLOCK_LANDSCAPE_START--->
```{r fig.cap="A boxplot", fig.id = "boxplot"}
ggplot(iris, aes(x = Sepal.Length, y = Sepal.Width, color = Species)) +
geom_boxplot()
```
```{r fig.width=10, fig.height=5, fig.id="plot", fig.cap="boxplot imported from images folder", echo=FALSE}
plot
```
<!---BLOCK_LANDSCAPE_STOP--->
Tips for working with plots/figures in Word output:
a) you need to use fig.height and/or fig.width to scale plots/figures;
b) consider using chunk option crop = TRUE with the function hook_pdfcrop() to trim/crop the extra white margin around the plot (see #CL. SO answer here);
c) chunk options: fig.align, fig.pos, out.height, out.width or out.extra are not supported for Word output.
To achieve desired output, you may consider the following changes:
```{r setup, include = FALSE, echo = FALSE}
pacman::p_load(readxl, dplyr, apastats, officedown, officer, ggplot2, knitr) # load packages
knitr::opts_chunk$set(fig.cap = TRUE,
fig.path = 'images/',
echo = FALSE,
warning = FALSE,
message = FALSE,
include = TRUE,
dpi = 300)
```
```{r}
# Creating a boxplot and saving it in \images directory
plot <- ggplot(iris, aes(x = Sepal.Length, y = Sepal.Width, color = Species)) +
geom_boxplot()
ggsave("images/plot.png", plot, dpi = 300)
```
```{r fig.id = "plot", fig.cap = "boxplot imported from images folder", fig.height = 6, fig.width = 7.5, echo = FALSE}
knitr::include_graphics("images/plot.png")
```
Does this helps somehow?
After implementing #David Gohel answer for a few projects. I still am envious of the use of out.height and out.width in PDF outputs.
In most of my projects I have resorted to going into File Explorer, right clicking on the figure in question and writing down the images dimensions to calculate its aspect ratio.
In a typical officedown project I will only call fig.width so that I can make sure the figure is maximized to the size of the page while maintaining its original aspect ratio.
knitr::include_graphics("images/plot.png")
I worked on trying to implement this automatically which would require reading the images dimensions to set fig.asp. Its not perfect, and I am sure someone else will have a much better and cleaner approach but you can accomplish this using the magick package. This also requires 2 chunks to accomplish the feat (again not optimal)
{r, eval=TRUE, echo=FALSE}
# First chunk to fetch the image size and calculate its aspect ratio
img <- magick::image_read("images/plot1.png") # read the image using the magic library
img.asp <- image_info(img)$height / image_info(img)$width # calculate the figures aspect ratio
{r fig.width=11, fig.asp = img.asp, fig.id="plot", fig.cap="boxplot imported from images folder", echo=FALSE}
# second chunk uses "img.asp" to make sure our aspect ratio is maintained.
knitr::include_graphics("images/plot.png")
I am creating a pdf with bookdown.
My problem is that I have the text between figures but it shows the text above the figures and the figures below one by one.
index.Rmd
---
title: "A title"
author: "George"
date: "`r Sys.Date()`"
output:
bookdown::tufte_book2: default
description: V
documentclass: book
link-citations: yes
bibliography: book.bib
site: bookdown::bookdown_site
biblio-style: apalike
---
02-explore.Rmd
# Explore {#explore}
```{r global, echo=FALSE, include=FALSE}
library(knitr)
knitr::opts_chunk$set(cache = TRUE, warning = FALSE, message = FALSE, tidy = FALSE,
fig.width = 6, fig.height = 4, dev = "cairo_pdf")
# list libraries and load data frame
```
Text goes here .
```{r title1, echo = FALSE, fig.cap = "One"}
ggplot
```
Another text .
```{r stw-title2, echo = FALSE, fig.cap = "Two"}
ggplot
```
output.yml
bookdown::tufte_book2:
includes:
in_header: preamble.tex
before_body: dedication.tex
after_body: after.tex
latex_engine: xelatex
citation_package: natbib
So, I want some text , first figure below , another text and another figure below, but instead I am receiving all text above all figures.
I found that if I use :
fig.width = 5 and fig.aps = 1/2 (or 1/3)
then the text and figures appear in the right order.
So, it was a problem with fig.height.
I am trying to style the word document using the Rmarkdown. I have successfully applied the basic styles by providing the reference word document under the YAML.
However, I am looking at some advanced styling like applying the different font size or colour to the paragraphs/headers in the same document.
Right now if I change the colour of any one paragraph to blue, colour of all the paragraphs get's changed to blue where I wanted to change the colour of only some of the paragraphs.
current rmarkdown:
---
title: "`r params$report_title`"
params:
report_title: NA
absolute_application_path: NA
output:
word_document:
md_extensions: +styles
reference_docx: "mmr_tec_report_reference-file.docx"
---
```{r setup, include=FALSE, echo=FALSE}
knitr::opts_chunk$set(echo = FALSE, warning = FALSE, message = FALSE)
library(pander)
```
```{r echo = FALSE}
application_path = params$absolute_application_path
signature_note <- ""
summary_note <- ""
```
## Template Instructions:
::: {custom-style="MMR_BodyText"}
The blue text are instructions or guidance for preparing the Sample or examples. Delete the blue highlighted instructions as the document is being drafted.
:::
Am I doing anything wrong up there?
I would like to know if there is any way to get it worked?
I am trying to use a download button in the input column of a flex dashboard to download a collection of charts rendered as *.pdf. The entire dashboard works just fine, and the download button renders properly; however, when I click the download button, the file that does get downloaded does not contain the intended charts. The warning I get from my Mac when it tries to open the file is that the file might be damaged or that it's a form that Preview (or Acrobat) doesn't recognize. The following is a highly redacted form of my code that contains the problematic sections. Any guidance on how to get charts to download in a flexdashboard as charts download in Shiny?
---
title: "My Model"
runtime: shiny
output:
flexdashboard::flex_dashboard:
theme: cerulean
vertical_layout: scroll
orientation: rows
---
```{r global, include=FALSE}
library(shiny)
library(shinyBS)
library(shinyWidgets)
library(flexdashboard)
library(tidyverse)
library(readxl)
library(knitr)
library(RColorBrewer)
source("MLHS_Distributions.R")
source("interp.R")
source("tooltips.R")
```
```{r Inputs}
downloadButton("downlaodReport","Price Comparision Report")
downloadHandler(filename = function() {
filename = paste0("ModelReport-", Sys.Date(), ".pdf")
},
content = function(file) {
pdf(file, width = 8.5, height = 6.14)
renderPrint({output$gg.prob.win.price()})
dev.off()
}
)
```
```{r priceProbWinChart}
renderPlot({
gg.prob.win.price <- --ggplot code--
plot(gg.prob.win.price)
})
```
I would like to create a Shiny-RMarkdown app which allows uploading own datasets. Datasets sometimes not only affect one chunk which can be re-rendered by renderPlot() (or similar) but sometimes two or more chunks. See the following example:
---
title: Render multiple chunks
output: html_document
runtime: shiny
---
```{r echo=FALSE}
library(shiny)
fileInput('file1', 'Choose your own CSV File instead of provided
data',accept=c('text/csv', 'text/comma-separated-values,text/plain',
'.csv'))
go1<-reactive({
dpath <- "CurrentBiologyData.txt"
if(!is.null(input$file1)){
dpath <- input$file1$datapath
}
CB.dat <- read.table(dpath, header = TRUE) #choose 'CurrentBiologyData.txt'
plot(CB.dat)
})
```
```{r echo=FALSE}
renderPlot({
go1()
})
```
```{r}
renderPlot({
print(CB.dat)
})
```
So I have three chunks which are affected if I upload a new dataset. The problem is that the third chunk does not see CB.dat which is filled in the first chunk:
Error: Object 'CB.dat' not found
Any ideas how I can make that work?
Applying to your example what I meant in my comment
Put the file reading in a reactive then use it wherever you need it
---
title: Render multiple chunks
output: html_document
runtime: shiny
---
```{r echo=FALSE}
library(shiny)
fileInput('file1', 'Choose your own CSV File instead of provided
data',accept=c('text/csv', 'text/comma-separated-values,text/plain',
'.csv'))
CB.dat<-reactive({
dpath <- "CurrentBiologyData.txt"
if(!is.null(input$file1)){
dpath <- input$file1$datapath
}
read.table(dpath, header = TRUE) #choose 'CurrentBiologyData.txt'
})
```
```{r echo=FALSE}
renderPlot(plot(CB.dat())
```
```{r}
renderTable(CB.dat())
```