I want to include a picture form the web in my markdown document, but I just want the left part of the picture. I searched on how to trim picture with rmarkdown but I found nothing...
Here is an example
---
title: "How to trim?"
output: html_document
---
```{r setup, include=FALSE}
library(knitr)
knitr::opts_chunk$set(echo = TRUE, fig.align = 'center')
```
Include picture
```{r pic}
include_graphics("http://ggplot2.tidyverse.org/README-example-1.png")
```
which gave me this HTML output.
If I want to trim the legend (the ~20% right part), how can I do?
I accept any type of answer: relative or absolute specifiation, rmarkdown or html solution, ...
Thanks!
You can use:
library(magick)
crop <- function(im, left = 0, top = 0, right = 0, bottom = 0) {
d <- dim(im[[1]]); w <- d[2]; h <- d[3]
image_crop(im, glue::glue("{w-left-right}x{h-top-bottom}+{left}+{top}"))
}
"http://ggplot2.tidyverse.org/README-example-1.png" %>%
image_read() %>%
crop(right = 210)
Thanks to #hrbrmstr comment, I found a solution.
library(magick)
library(magrittr)
image_read("http://ggplot2.tidyverse.org/README-example-1.png") %>%
image_flop() %>%
image_crop("1344x960+250") %>%
image_flop()
I'm not sure it's the most efficient with the two image_flop() functions and I don't understand precisly the "1344x960+250" but it works :)
Related
My code is producing a lot of NULLs at the end in the html output.
Could you please help me to prevent it?
---
title: "Test"
output: html_document
---
```{r warning=FALSE, message=FALSE, results = 'asis',echo=FALSE}
library(tidyverse)
library(knitr)
library(kableExtra)
# nest all data except the cut column and create html tables
diamonds_tab <- diamonds %>%
nest(-cut) %>%
mutate(tab = map2(cut,data,function(cut,data){
writeLines(landscape(kable_styling(kable(as.data.frame(head(data)),
caption =cut,
format = "html",align = "c",row.names = FALSE),
latex_options = c("striped"), full_width = T)))
}))
# print tab column, which contains the html tables
invisible(walk(diamonds_tab$tab, print))
```
Instead of using invisible, wrap the print command with capture.output.
---
title: "Test"
output: html_document
---
```{r warning=FALSE, message=FALSE, results = 'asis',echo=FALSE}
library(tidyverse)
library(knitr)
library(kableExtra)
# nest all data except the cut column and create html tables
diamonds_tab <- diamonds %>%
nest(-cut) %>%
mutate(tab = map2(cut,data,function(cut,data){
writeLines(landscape(kable_styling(kable(as.data.frame(head(data)),
caption =cut,
format = "html",align = "c",row.names = FALSE),
latex_options = c("striped"), full_width = T)))
}))
# print tab column, which contains the html tables
walk(diamonds_tab$tab, ~ capture.output(print(.x)))
```
I found out, that it is only enough to remove the walk.
EDIT: Because I had set the format options in a global function, I have to set either latex_options or bootstrap_options in the kable_styling() call. I was using bootstrap_options which wasn't being read by the latex. My work-around is to make the tables twice, once in a chunk for html, and once in a chunk for latex. Not great, but it works if I click the Knit button and choose Knit to PDF. However, it throws the original error when I try to run it in the shiny app.
I have created a test version (MiniTest) of my project. What I need to do is have a shiny app run with a tab that will produce an html file for a user-chosen (reactive) Country, and provide an Excel download (I have that working so kept it out of this example), and a PDF download. I knit in an .Rmd which chooses the format and allows for parameterization. (The shiny part was set up by someone else, from whom I took over this project when they left before finishing it.)
I use kable and kableExtra to create and format tables, as I heard it words for both html and LaTeX output. The HTML is more as less as I want it. I can knit either html or PDF, and it runs, BUT when in the shiny app, only the html portion works. I think I have narrowed down the PDF issue(s) to column_spec crashing the download. If I comment out the column_spec lines in t01 and t02, the Download PDF runs. But I need that formatting. I'm sorry, but I've lost track of all the sites I have searched.
In global.R, I set:
countries <- c("ABC", "DEF", "GHI", "JKL")
In the .Rmd, I have YAML set up (with two-space indents for Country and output types):
params:
Country: ABC
output:
pdf_document: default
html_document: default
Relevant .Rmd chunks and inline code include:
knitr::opts_chunk$set(echo = FALSE)
options(knitr.table.format = function() {
if (knitr::is_latex_output()) "latex" else "html"
})
library(shiny)
library(htmlwidgets)
library(shinythemes)
library(shinydashboard)
library(shinyjs)
library(shinycssloaders)
library(markdown)
library(tidyr)
library(tidyverse)
library(janitor)
library(kableExtra)
options(scipen = 999)
mini <- mtcars %>%
tibble::rownames_to_column(var = "car") %>%
mutate(Country = c(rep("ABC", 8), rep("DEF", 8), rep("GHI", 8), rep("JKL", 8)))
## https://bookdown.org/yihui/rmarkdown-cookbook/font-color.html
colorize <- function(x, color) {
if (knitr::is_latex_output()) {
## hack setting color='blue' instead of a hexcode with # that breaks the LaTeX code
sprintf("\\textcolor{%s}{%s}", color = 'blue', x) ## works, but isn't right blue
} else if (knitr::is_html_output()) {
sprintf("<span style='color: %s;'>%s</span>", color, x)
} else x
}
## make two tables with `kable` and `kableExtra`
new_title <- paste0("Dynamically Changing Country Name in column", params$Country)
t01 <- mini %>%
filter(Country == params$Country) %>%
select(car, mpg:hp) %>%
rename({{new_title}} := car) %>%
kable(align = c("l", "c", "c", "c", "c")) %>%
kable_styling(full_width = FALSE, position = "left", bootstrap_options = c("striped", "condensed")) %>%
column_spec(1, bold = TRUE) %>%
column_spec(2:3, width = "5em") %>%
row_spec(0, color = "#2A64AB") %>%
row_spec(6, bold = TRUE)
t02_title <- paste0(params$Country, " Table with Dollar Signs in Var Names")
t02 <- mini %>%
filter(Country == params$Country) %>%
select(car, drat, wt) %>%
mutate(car = case_when(car == "Mazda RX4" ~ "Mazda RX4 (US\\$)*", TRUE ~ as.character(car))) %>%
## want to blank out column names - removing them entirely would be best, but it fails
kable(align = c("l", "r", "c"), escape = TRUE, col.names = c("", "", "")) %>%
kable_styling(full_width = FALSE, position = "left", bootstrap_options = c("striped", "condensed")) %>%
column_spec(1, bold = TRUE) %>%
column_spec(2, width = "10em") %>%
footnote(general = "*Never smart to start with an asterisk, but here we are", general_title = "")
## make two charts with `ggplot2`
chart1 <- mini %>%
filter(Country == params$Country) %>%
select(car, mpg:hp) %>%
ggplot2::ggplot(mapping = aes(x = mpg)) +
geom_col(aes(y = `cyl`, fill = "cyl"), color = "black")
c1_title <- paste0("Some fab title here for ", params$Country)
chart2 <- mini %>%
filter(Country == params$Country) %>%
select(car, vs:carb) %>%
ggplot2::ggplot(mapping = aes(x = carb)) +
geom_col(aes(y = `gear`, fill = "gear"), color = "black")
c2_title <- paste0("Another chart, ", params$Country)
## make a "tiny" LaTeX environment that is only generated for LaTeX output, with chunk setting `include = knitr::is_latex_output()`.
knitr::asis_output('\n\n\\begin{tiny}')
## Table 1
t01
I expect a PDF to pop up, but instead a Save File box pops up asking to save "DownloadPDF" with no file extension. The ui.R is supposed to name it as "FactCountryName.pdf" where "CountryName" is input from the Country the user chose in the drop-down list. Regardless of whether I choose Save (nothing happens) or Cancel, my R throws the following error:
```
! LaTeX Error: Illegal character in array arg.
```
If I comment out the line column_spec(1, bold = TRUE) %>%, the error changes to:
```
! Use of \#array doesn't match its definition.
\new#ifnextchar ...served#d = #1\def \reserved#a {
#2}\def \reserved#b {#3}\f...
l.74 ...m}|>{\centering\arraybackslash}p{5em}|c|c}
```
Please help!
Turns out that using the Knit button in R automatically loads the required LaTeX packages, such as booktabs. Running the file in the Shiny app was not loading all the packages needed. All I had to do was specifically call the extra packages in the YAML (which I found by looking at the .tex file made from the PDF through Knit button).
---
params:
Country: ABC
header-includes:
- \usepackage{booktabs}
- \usepackage{longtable}
- \usepackage{array}
- \usepackage{multirow}
- \usepackage{wrapfig}
- \usepackage{float}
- \usepackage{colortbl}
- \usepackage{pdflscape}
- \usepackage{tabu}
- \usepackage{threeparttable}
- \usepackage{threeparttablex}
output:
pdf_document:
keep_tex: true
html_document: default
---
Question about knitting RMarkdown.
I am having issues when knitting a Rmarkdown file to HTML/pdf. When I run my chunks of code in the Rmarkdown file everything runs smoothly (and I get my graphs made with ggplot) but when knitting I get an output with no graphs and errors (error in eval, error in ggplot, error in print).
Does anyone have experience with this?
The errors:
Error in eval(lhs, parent): object ‘iso3166’ not found
Error in ggplot(inci_100k, aes(long, lat, map.id=mapname,fill=inci)): object ‘inci_100k’ not found
Error in print(INCIPLOT): object ‘INCIPLOT’ not found
The code:
---
title: "R Markdown MAP"
author: "Alexandra V"
date: "1/4/2020"
output:
html_document: default
pdf_document: default
word_document: default
---
```{r,echo = FALSE, warning = FALSE, message=FALSE, error=TRUE}
knitr::opts_chunk$set(cache=TRUE)
knitr::opts_chunk$set(echo = TRUE)
knitr::opts_chunk$set(error = TRUE)
```
Loading the packages we will need for the following analysis.
```{r echo=FALSE, warning=FALSE}
library(tidyverse)
library(lubridate)
library(ggmap)
library(countrycode)
library(grid)
library(gridExtra)
```
To only keep the data needed to make a worldmap of TB incidences, only the relevant data will be taken from the TB_burden_countries_2020-01-04.csv file. Column 1: country names, column 3: iso3 (country codes), column 6: years, column 8: e_inc_100k (estimated incidence all TB forms per 100.000). To make the file easier to work with the names of the columns will be changed to: country, code, year and inci respectively.
```{r, message=FALSE}
TB.burden <- read.csv("TB_burden_countries_2020-01-04.csv")
TBworldINC.map <- as.data.frame(TB.burden[,c(1,3,6,8)], drop=false)
write.csv(TBworldINC.map, 'TBworldINC.map.csv', row.names = FALSE)
tb.INC <- read_csv("TBworldINC.map.csv") %>%
setNames(c("country", "code", "year", "inci"))
```
```{r}
world <- map_data("world")
tb_some_years <- tb.INC %>%
filter(year %in% c(2005, 2010, 2015, 2018))
inci_100k <- tb_some_years %>%
inner_join(iso3166 %>% select(a3, mapname), by = c(code = "a3")) %>%
left_join(world, by = c(country = "region"))
INCIPLOT <- ggplot(inci_100k, aes(long, lat, map_id = mapname,
fill = inci)) +
geom_map(map = world) +
scale_fill_gradient(low = "blue", high = "yellow") +
theme_void() +
coord_map(xlim = c(-180, 180)) +
labs(fill = "Incidence per year") +
facet_wrap(~ year, ncol = 2)
print(INCIPLOT)
```
picture of the output I get in Rstudio
I have had similar issues when making maps in R. One work around is to create your graphs and to save it locally and including the images. The syntax for adding images in R Markdown is 
Im creating a flexdashboard which displays a table. In the last column icons are included but they are not displayed at all because of flexdashboard. That works normally in shinydashboard. Any workaround?
---
title: "Single Column (Fill)"
output:
flexdashboard::flex_dashboard:
vertical_layout: fill
---
```{r global, include=FALSE}
library(shiny)
library(shinydashboard)
FCB<-c(5,6,4,6,8)
TWI<-c(3,5,2,3,5)
IN<-c(2,1,1,1,1)
DF1<-data.frame(FCB,TWI,IN)
FCB<-c(0,0,1,2,4)
TWI<-c(1,2,3,4,5)
IN<-c(1,3,4,5,6)
DF2<-data.frame(FCB,TWI,IN)
DF1$direction <- ifelse(
DF1$FCB < DF2$FCB,
as.character(icon("angle-up")),
as.character(icon("angle-down"))
)
```
### Chart 1
```{r}
renderTable(DF1, sanitize.text.function = function(x) x)
```
You are using Shiny content rendered to a static file.
I added runtime: shiny to the YAML header.
If you just need arrows would using simpe UTF-8 arrows like these be okay?
If you want to render HTML in a table in flexdashboard you should use a datatable from the DT package. Note that the rendering of the HTML is escaped by default. To render the HTML in your table you have to set escape = FALSE.
Here is an option:
---
title: "Single Column (Fill)"
output:
flexdashboard::flex_dashboard:
vertical_layout: fill
runtime: shiny
---
```{r global, include=FALSE}
library(DT)
library(shiny)
library(shinydashboard)
FCB<-c(5,6,4,6,8)
TWI<-c(3,5,2,3,5)
IN<-c(2,1,1,1,1)
DF1<-data.frame(FCB,TWI,IN)
FCB<-c(0,0,1,2,4)
TWI<-c(1,2,3,4,5)
IN<-c(1,3,4,5,6)
DF2<-data.frame(FCB,TWI,IN)
DF1$direction <- ifelse(
DF1$FCB < DF2$FCB,
"<p>↑</p>",
"<p>↓</p>"
)
DF1.table <- datatable(DF1, escape = FALSE)
```
### Chart 1
```{r}
DT::renderDataTable(DF1.table)
```
I have an R Markdown document, with an R chunk containing 2 lines of code. In the resulting HTML document, I would like all the code lines belonging to the same chunk (two in this example) to be printed in a single box, before their output.
---
title: "Just a test"
author: "Yours Truly"
date: '`r Sys.Date()`'
output:
html_document:
fig_caption: yes
---
```{r setup, include=FALSE}
library(ggplot2)
library(car)
library(knitr)
opts_chunk$set(cache = TRUE,
out.width = "75%",
fig.align = "center")
```
here is some code
```{r EDA}
summary(Davis)
ggplot(Davis, aes(x = height, y = weight)) +
geom_point()
```
Instead, what I get is that each line of code of the chunk is immediately followed by its output:
I want the two gray boxes containing summary(Davis) and ggplot(Davis, aes(x = height, y = weight)) + geom_point() to be joined together in a single gray box, followed by their output. Is this possible?