R Markdown List of Kabels output to PDF - r

I have a 500 x 500 dataset which I would like to be represented in kables in my PDF output. I've arbitrarily chosen 50 x 50 Kables for the output.
Each kabel cell will have an image in it^. Some of these examples will work with pure text so including the image is required in the minimum code.
In the code below, there is the setup and the 3 approaches I've taken:
the 500x500 approach which is obviously too big,
the list method which I can't get to actually render the tables,
the separate, dynamically named, objects^ approach which will render a table if called by exact name but can't get to render from a dynamic name.
The generation of the kables are in different code chunks to the output for ease of positioning in the PDF.
I have tried all these with results = 'asis' and it made no difference.
---
title: "Minimum Example"
date: "2022-11-19"
output: pdf_document
---
\section*{A Bit of Setup}
\renewcommand{\arraystretch}{1.7}
```{r setup}
library(kableExtra)
library(dplyr)
library(tidyr)
library(stringr)
library(png)
library(knitr)
# Image is displayed in each cell of the Kable, creating an example image
png(file="./ExampleImage.png")
par(bg='grey')
bob <- plot.new()
dev.off()
# Define size of data which needs to be represented in a kable.
totalSize_x <- 500
totalSize_y <- 500
```
\section*{Approach 1: Way too big to be displayed}
```{r Approach 1: The Big Boy}
TheBigBoi <- matrix('\\includegraphics[scale=1]{./ExampleImage.png}',totalSize_x, totalSize_y)
kable(TheBigBoi,
format = "latex",
escape = FALSE,
longtable = FALSE) |>
column_spec(1,border_left = T) |>
column_spec(totalSize_y,border_right = T) |>
kable_styling(latex_options=c("scale_down"))
# Gives the Errors
# Error: C stack usage 12426279 is too close to the limit
# Execution halted
```
\section*{Approach 2: A Nice List}
```{r Approach 2: A Nice List}
# Personally, I want this one to work as it's the least stupid solution.
maxKableCells <- 50 # As in that looks good for the images, I understand Kables can be bigger if they want to
TheLittleOne <- matrix('\\includegraphics[scale=1]{./ExampleImage.png}', maxKableCells, maxKableCells)
num_iterations <- (totalSize_x/maxKableCells) * (totalSize_y/maxKableCells)
myList <- vector(mode = "list", length = num_iterations)
for (i in 1:(num_iterations)){
myList[i] <- kable(TheLittleOne,
format = "latex",
escape = FALSE,
longtable = FALSE) |>
column_spec(1,border_left = T) |>
column_spec(maxKableCells,border_right = T) |>
kable_styling(latex_options=c("scale_down"))
}
```
Gonna put some text here
```{r Approach 2 Output}
myList[1] # - ! Undefined control sequence.
#l.177 ``\textbackslash begin\{table\}\n
# \textbackslash centering\n\textbacksl...
```
```{r Approach 2 Output Continued}
noquote(myList[1]) # - just prints out the latex code with extra slashes
```
\section*{Approach 3: Objectively the worst way to acheive this}
```{r Approach 3: Individual Kable Objects AKA Foolishness}
# The most stupid solution but the closest to working
maxKableCells <- 50 # As in that looks good for the images, I understand Kables can be bigger if they want to
TheLittleOne <- matrix('\\includegraphics[scale=1]{./ExampleImage.png}', maxKableCells, maxKableCells)
num_iterations <- (totalSize_x/maxKableCells) * (totalSize_y/maxKableCells)
for (i in 1:(num_iterations)){
assign(paste0('kable_', i), kable(TheLittleOne,
format = "latex",
escape = FALSE,
longtable = FALSE) |>
column_spec(1,border_left = T) |>
column_spec(maxKableCells,border_right = T) |>
kable_styling(latex_options=c("scale_down")))
}
```
Some filler text
```{r Approach 3 Output}
kable_1 # - This one works!
for (i in 1:num_iterations){
paste0('kabel_', i) #Returns nothing
print(paste0('kabel_', i)) # Prints like "kabel_1"
print(noquote(paste0('kabel_', i))) #Prints like kabel_1
noquote(paste0('kabel_', i)) # Returns nothing
}
```
^ I am aware this is a stupid thing to do, this whole thing is stupid but sometimes the tools we use are not our own choice.

Related

Scientific formats, subscripts and superscripts in RMarkdown table (docx output)

Let's say I have the following rmd:
---
title: "Table won't work"
author: "Exhausted student"
date: "2022/01/28"
output:
bookdown::word_document2
---
```{r table, echo=F, warning=F, message=F}
library(tidyverse)
a <- tibble(
constants = c("c", "NA", "h", "e", "H2O"),
values = c(2.998e8, 6.022e23, 6.626e-34, -1.602e-19, 18.02)
)
knitr::kable(a, digits = 35)
```
which produces this table in Word.
The Problem
I need the scientific format to use superscripts and multiply sign (i.e. 2.998 × 108), and some cells requires subscript (e.g. NA and H2O).
The final table should look like this. How can I do that?
What I've tried/would never try
huxtable package and its markdown() function: I managed to format some contents as H~2~O, then enable markdown across table by huxtable(a) %>% `markdown<-`(TRUE). Which did not recognize the syntax, and apparently would not work in forseeable future according to the author.
flextable and as_sub(): Produces right format. I pass the lables to flextable::compose(), where the labels were something like as_paragraph(list_values = list("H", as_sub("2"), "O"). The code is obviously too lengthy; plus i have to manipulate cells one-by-one. Technically still doable, but I do have tables with 100+ cells needed formatting.
Output first, format in Word later: Again, needed manipulation one-by-one. Would be an option if it would work everything out automatically.
Convincing the school bureaucrats to accept html/pdf/latex as output: this is forever an impossible option.
Format outside word then export formatted table as image: strictly forbidden in the reports.
Edit: the table works now! Great thanks to Maël's answer, but please check my own findings to see my final result:
You can use tildes (~) to put in subscript and carets (^) for superscripts; and use sprintf to get the expected digit format:
---
title: "Table won't work"
author: "Exhausted student"
date: "2022/01/28"
output:
bookdown::word_document2
---
```{r table, echo=F, warning=F, message=F}
library(tidyverse)
expSup <- function(x, digits=3) {
sprintf(paste0("%05.", digits, "f x 10^%d^"), x/10^floor(log10(abs(x))), floor(log10(abs(x))))
}
a <- tibble(
constants = c("c", "N~A~", "h", "e", "H~2~0"),
values = expSup(c(2.998e8, 6.022e-23, 6.626e-34, -1.602e-19, 18.02))
)
knitr::kable(a)
```
An option that probably falls in the no-go zone for this open issue:
Create a html document,
Insert html tags for subscripts,
Open the html file (not the viewer),
ctrl+c, then ctrl+v in your word file.
---
output: html_document
---
```{r table, echo=F, warning=F, message=F}
library(tidyverse)
library(gt)
a <- tibble(
constants = c("c", "N<sub>A</sub>", "h","e","H<sub>2</sub>O"),
values = c(2.998e8, 6.022e23, 6.626e-34, -1.602e-19, 18.02)
)
a %>%
mutate(constants = map(constants, html)) %>%
gt() %>%
fmt_scientific(values)
The expSup() function in Maël's answer converted the scientific formats into markdown format. For my script, I modified the function a little:
exp_sup <- function(x, digits = 3) {
sprintf(paste0("%05.", digits, "f $\\times$ 10^%d^"), x / 10^floor(log10(abs(x))), floor(log10(abs(x))))
}
I changed "f x 10^%d^" to "f $\\times$ 10^%d^", so that it displays proper multiply symbol (×).
Using the format in flextable
The format works great in Kable. However, a large portion of my workflow requires flextable to make caption/cross reference/publication style/etc. Unfortunately, although the expSup function automatically formats scientific notations into markdowns, it cannot make markdown syntax work in flextable.
However, ftExtra::colformat_md() can. Hence, by combining the modified exp_sup() function with ftExtra, I was finally able to produce an academic-looking table:
Below is the code for my final output; if you are also trying to produce reproducible academic reports with lots of tables in Word format, hope this helps!
---
title: "The tables work!"
author: "Satisfied Student"
date: "2022/01/28"
output:
bookdown::word_document2:
reference_docx: styleRef.docx
---
```{r setup, include = F}
library(easypackages)
packages(
"tidyverse",
"flextable", # This works best for my workflow
"ftExtra", # For markdown formatting work in flextable
"officer" # You can customize appearance/format/etc. of caption *prefixes*
)
knitr::opts_chunk$set(
warning = FALSE,
message = FALSE,
echo = FALSE,
# Make the table caption format definable in reference_docx styles
tab.cap.style = "Table Caption",
# Make "Table 1:" prefixes not bold
tab.cap.fp_text = fp_text_lite(bold = FALSE)
# The tab.cap settings MUST be in a separate chunk from tables
)
# Converts scientific format to markdown
exp_sup <- function(x, digits = 3) {
sprintf(paste0("%05.", digits, "f $\\times$ 10^%d^"), x / 10^floor(log10(abs(x))), floor(log10(abs(x))))
}
# The $\\times$ makes proper multiply symbols
```
```{r table}
a <- tibble(
constants = c("c", "N~A~", "h", "e", "H~2~O"),
values = c(2.998e8, 6.022e23, 6.626e-34, -1.602e-19, 18.02)
)
a %>%
mutate(values = exp_sup(values)) %>%
flextable() %>%
set_caption(
caption = "(ref:foo)", # Produces formatted caption text
style = "Table Caption"
) %>%
colformat_md() %>% # Subscript/superscript works in flextable now!
theme_booktabs() %>% # The 3-part-table used in academics
align(align = "center", part = "all") %>% #Align everything to center
set_table_properties(layout = "autofit") # Comfortable width/height every cell
```
(ref:foo) A scientifically formatted `flextable` with ^superscripts^ and ~subscripts~
Your code should look like this:
```
{r table, echo=F, warning=F, message=F}
library(tidyverse)
a <- tibble(
constants = c("c", "NA", "h", "e", "$H_2O$"),
values = c("$2.998 * {10^{8}}$", "$6.022 * {10^{-23}}$", "$6.626 * {10^{-34}}$", "$-1.602 * {10 ^{-19}}$", "$1.802 * {10^{1}}$")
)
knitr::kable(format = "html", a, digits = 35)
```
Which will give you the output like this:

kableExtra : How can i set to bold the biggest value of the row?

Suppose i have a table that looks like :
x = matrix(runif(10*5),nrow=10,ncol=5)
When i display the matrix using kableextra, i want the highest value, per row, of say the last 2 rows, to be bolded.
I looked at this document https://rdrr.io/cran/kableExtra/f/inst/doc/awesome_table_in_pdf.pdf a lot and i did not found how to use cell_spec correctly to perform this goal.
I thought this would be easier than it turned out to be. As far as I can see, this is how to do it:
---
title: "Untitled"
output: pdf_document
---
```{r}
set.seed(123)
library(knitr)
library(kableExtra)
x <- matrix(round(runif(10*5),2), nrow=10,ncol=5)
j1 <- which.max(x[9,])
j2 <- which.max(x[10,])
col <- seq_len(ncol(x))
x[9,] <- x[9,] %>% cell_spec(bold = col == j1)
x[10,] <- x[10,] %>% cell_spec(bold = col == j2)
x %>% kable(booktabs = TRUE, escape = FALSE)
```
A few notes:
I rounded the values so they aren't so ugly when printed.
I couldn't see a way to do everything in one pipeline, though there probably is one. The trouble is that cell_spec is designed to work on vectors, not matrices.
Finally, the escape = FALSE in kable() is essential: otherwise you'll see the code to make it bold, rather than the bold entry itself.

knitr changes (1) to <ol> when rendering html?

The following content of a .Rmd file:
---
title: "Untitled"
output:
html_document: default
---
```{r cars}
mtcars$am <- sprintf("(%s)", as.character(mtcars$am))
knitr::kable(mtcars, format = "html")
```
Will show ordered lists <ol><li></li></ol> in the am column, instead of the numbers in brackets (as produced with the sprintf) after rendering to html.
Is this intended? How can I work around this and have numbers in brackets show as they are in the html output?
The output of knitr::kable seems to be fine, showing:
<td style="text-align:left;"> (1) </td>
Details:
Using knitr 1.20
RStudio Server 1.1.453
note that removing format = "html" does not resolve the issue as in the real-life context I would like to do advanced formatting with css e.g. based on the classes of the produced tables
A quick workaround solution based on Michael Harper's accepted answer may be a method like so:
replacechars <- function(x) UseMethod("replacechars")
replacechars.default <- function(x) x
replacechars.character <- function(x) {
x <- gsub("(", "&lpar;", x, fixed = TRUE)
x <- gsub(")", "&rpar;", x, fixed = TRUE)
x
}
replacechars.factor <- function(x) {
levels(x) <- replacechars(levels(x))
x
}
replacechars.data.frame <- function(x) {
dfnames <- names(x)
x <- data.frame(lapply(x, replacechars), stringsAsFactors = FALSE)
names(x) <- dfnames
x
}
Example use:
mtcars <- datasets::mtcars
# Create a character with issues
mtcars$am <- sprintf("(%s)", as.character(mtcars$am))
# Create a factor with issues
mtcars$hp <- as.factor(mtcars$hp)
levels(mtcars$hp) <- sprintf("(%s)", levels(mtcars$hp))
replacechars(mtcars)
If you don't want to remove the format="html" argument, you could try using the HTML character entities for the parentheses (&lpar and &rpar) and then add the argument escape = FALSE:
```{r cars}
mtcars$am <- sprintf("&lpar;%s&rpar;", as.character(mtcars$am))
knitr::kable(mtcars, format = "html", escape = FALSE)
```
Still not entirely sure of what is causing the error though. It seems that the specific combination of parentheses is being processed strangely by knitr.
An alternative solution is to escape the parentheses, e.g.,
mtcars$am <- sprintf("\\(%s)", as.character(mtcars$am))
Then you won't need escape = FALSE.
See https://pandoc.org/MANUAL.html#backslash-escapes in Pandoc's Manual.

Using pre-generated character strings with index method for kableExtra group_rows

Using Rmarkdown to generate a PDF. I'm bringing in lengthy text strings generated from a prior function to use as grouped row labels in a table. The normal kableExtra::group_rows method works fine. Since I have the same number of rows in each group, I'd like to use the index method, but that doesn't seem to work:
---
output:
pdf_document:
latex_engine: xelatex
fig_caption: true
---
```{r}
library(magrittr)
library(knitr)
library(kableExtra)
# Build some data
df <- data.frame(x=1:12, y=13:24, z=25:36)
# Row grouping text gets generated from a separate function
gtext <- c("Group 1: text that I don't want to write out",
"Group 2: because it gets generated from something else",
"Group 3: so let's make life easy")
# This works fine:
df %>%
kable(format="latex", booktabs = TRUE, row.names=FALSE) %>%
group_rows(gtext[1],1,4) %>%
group_rows(gtext[2],5,8) %>%
group_rows(gtext[3],9,12)
# But this doesn't:
df %>%
kable(format="latex", booktabs = TRUE, row.names=FALSE) %>%
group_rows(index=c(gtext[1]=4,
gtext[2]=4,
gtext[3]=4))
```
I get the following error upon knitting: "Error in parse(text = x, srcfile = src) : :23:30: unexpected '=' 22:"
Over the course of 40+ tables with some that have up to 10 row groupings, it's easy to see how the index method would save time and prevent errors. Added functionality here (or a workaround that I may have missed) would be most excellent!
I could render this document to html by using
group_rows(index=setNames(c(4, 4, 4), gtext))
The issue appears to be the way you are attempting to create the named vector for the index argument. If you try this in the console, you'll get an error:
c(gtext[1] = 4, gtext[2] = 4, gtext[3] = 4)
While this does not:
setNames(c(4, 4, 4), gtext)
#> Group 1: text that I don't want to write out
#> 4
#> Group 2: because it gets generated from something else
#> 4
#> Group 3: so let's make life easy
#> 4

How to rotate a table left margin name with knitr and xtable?

I'm trying to get the results of the table command nicely printed on a pdf by using knitr and xtable.
As a toy example let's say I want to get the table created with
table(c(2,5,5,5,5,7,7,7,7,NA),c(1,5,2,2,2,2,7,7,NA,NA))
I would like to get something like this:
As you can see var1 is rotated 90 degrees counterclockwise.
How can I get it?
Similar results, with less or more lines are OK too.
I've being trying different methods I've found.
I've created this Rnw file,
\documentclass{article}
\usepackage{booktabs}
\usepackage{rotating}
\begin{document}
<<r table, results='asis', echo=FALSE>>=
library(knitr)
library(xtable)
var1 <- c(2,5,5,5,5,7,7,7,7,NA)
var2 <- c(1,5,2,2,2,2,7,7,NA,NA)
print(xtable(table(var1,var2)))
print.xtableFtable(xtableFtable(ftable(var1,var2),
method = "row.compact"))
print.xtableFtable(xtableFtable(ftable(var1,var2),
method = "row.compact"), rotate.rownames = TRUE)
print.xtable(xtable(table(var1,var2)), include.rownames=T,include.colnames=T)
#
\end{document}
You can see below the result of the three methods I've tried.
I can't get the expected result.
Any solution with other common package or kable it's OK too.
I guess it could be done with \rotatebox{90} but I don't know how to force xtable to use it nor how to tell xtable to place the left title on the left instead of just being on the top-right.
Here's one possibility. Disclaimer: I am the package author.
library(huxtable)
var1 <- c(2,5,5,5,5,7,7,7,7,NA)
var2 <- c(1,5,2,2,2,2,7,7,NA,NA)
tbl <- table(var1 = var1, var2 = var2)
ht <- as_hux(tbl)
ht <- cbind(rep('', 4), ht)
ht[2,1] <- 'var1'
ht <- rbind(rep('', 6), ht)
ht[2,2] <- '' # get rid of "rownames"
ht[1,3] <- 'var2'
colspan(ht)[1,3] <- 4
rowspan(ht)[3, 1] <- 3
rotation(ht)[3, 1] <- 90
right_border(ht)[,2] <- 1
bottom_border(ht)[5, -1] <- 1
bottom_border(ht)[2, -1] <- 1
ht
When used in an rmarkdown PDF document, this produces:

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