CODEWITHSUNDEEP
rr-markdownpandocpander
llewmills
llewmills

Reputation: 3568

Italicising the headings of a dataframe in rmarkdown

I would like to apply some latex-style formatting to column headings in a pander table in rmarkdown, knitting to pdf.

Notice in the toy document below the latex commands that work for the elements of the dataframe do not work for the headings. Specifically I would like (1) to be able to italicise some headings, (2) to be able to have headings with spaces between the letters (at the moment R automatically adds a .). However I am generally interested in how to get the headings in a dataframe to accept the same latex commands as the elements of the dataframe.

 ---
title: "Chapter 12: Adding to the Discrete Time Hazard Model"
output:
  pdf_document: default
  html_document: null
  word_document: null
toc: yes
linestretch: 1.3
classoption: fleqn
header-includes: 
 - \setlength{\mathindent}{0pt}
 - \setlength\parindent{0pt}
 - \usepackage{amssymb}
---

```{r global_options, include=FALSE, echo = FALSE}
#this sets global knit options (i.e. options for the entire document. The following supresses any warnings from being include in the output and sets plot parameters. Note that setting dev to pdf allows us to set size of graphs easily
rm(list = ls())

knitr::opts_chunk$set(fig.width=12, fig.height=8, fig.path='Figs/', 
                      echo=FALSE, warning=FALSE, message=FALSE, dev = 'pdf')
```

``` {r table p 446}
abC <- 0.3600344
bC <- 0.2455304 
intC <- 0.4787285


dfTrans <- data.frame("Prototype" = c("$\\textit{Left/not Blue}$", "Left/Blue", "Right/not Blue", "Right/Blue"),
                      "$LEFT$" = c(0,1,0,1),
                      "$\\textit{BLUE}$" = c(0,0,1,1),
                      `Combined Parameter Estimates` = c(paste("0 x ", round(abC,4), "+ 0 x", round(bC,4), "+ 0 x", round(intC, 4), sep = " "),  8, 9, 0))


library(pander)
panderOptions('table.split.table', 300) # this forces the table to the width of the page. 
pander(dfTrans, justify = "left")
```

Upvotes: 2

Views: 1024

Answers (2)

eipi10
eipi10

Reputation: 93821

I'm not sure how to do this with pander, but here is a method using the kable function from knitr and kableExtra functions for detailed table formatting. I haven't changed the yaml markup, but the updated code chunks are pasted in below, followed by the output.

```{r global_options, include=FALSE, echo = FALSE}
#this sets global knit options (i.e. options for the entire document. The following supresses any warnings from being include in the output and sets plot parameters. Note that setting dev to pdf allows us to set size of graphs easily
knitr::opts_chunk$set(fig.width=12, fig.height=8, fig.path='Figs/', 
                      echo=FALSE, warning=FALSE, message=FALSE, dev = 'pdf')

# rm(list = ls()) This is unnecessary. knitr runs the rmarkdown document in a clean session.

library(knitr)
library(kableExtra)
options(knitr.table.format = "latex")  # latex output (instead of default html)
library(tidyverse) # For dplyr pipe (%>%) and mutate
```

```{r table p 446}
abC <- 0.3600344
bC <- 0.2455304 
intC <- 0.4787285

# I've removed the latex formatting from the data frame code
dfTrans <- data.frame(Prototype = c("Italic_Left/not Blue", "Left/Blue", "Right/not Blue", "Right/Blue"),
                      LEFT = c(0,1,0,1),
                      BLUE = c(0,0,1,1),
                      `Combined Parameter Estimates` = c(paste("0 x ", round(abC,4), "+ 0 x", round(bC,4), "+ 0 x", round(intC, 4), sep = " "),  8, 9, 0))

# Remove periods in column names
names(dfTrans) = gsub("\\.", " ", names(dfTrans))
# Two other options: 
# 1. Use the data_frame function from tidyverse, rather than the base data.frame function. 
#    data_frame doesn't add periods, so you won't need to fix the column names afterwards.
# 2. Set check.names=FALSE in data.frame

# Use kableExtra cell_spec function to format on a cell-by-cell basis
dfTrans = dfTrans %>% 
  mutate(Prototype = cell_spec(Prototype, color=c("black","blue"),
                               align=rep(c("l","r"), each=2)))

# Format each of the column names using kableExtra text_spec
names(dfTrans)[1] = text_spec(names(dfTrans)[1], italic=TRUE)
names(dfTrans)[2] = text_spec(names(dfTrans)[2], align="l")
names(dfTrans)[3] = text_spec(names(dfTrans)[3], align="r", italic=TRUE, color="blue")
names(dfTrans)[4] = text_spec(names(dfTrans)[4], align="r")

# Output the table
kable(dfTrans, booktabs=TRUE, escape=FALSE) 
```

enter image description here

One thing I'm not sure how to do yet is to format just the first value of dfTrans$Prototype as italic. cell_spec seems to use only the first value of an italic logical vector, so the following italicizes the whole column:

dfTrans = dfTrans %>% 
  mutate(Prototype = cell_spec(Prototype, color=c("black","blue"),
                               align=rep(c("l","r"), each=2),
                               italic=c(TRUE, rep(FALSE, n()-1))))

Upvotes: 4

user3603486
user3603486

Reputation:

Here is a huxtable-based solution (my package):

abC  <- 0.3600344
bC   <- 0.2455304 
intC <- 0.4787285
dfTrans <- data.frame(Prototype = c("Italic_Left/not Blue", "Left/Blue", "Right/not Blue", "Right/Blue"),
                  LEFT = c(0,1,0,1),
                  BLUE = c(0,0,1,1),
                  `Combined Parameter Estimates` = c(paste("0 x ", round(abC,4), "+ 0 x", round(bC,4), "+ 0 x", round(intC, 4), sep = " "),  8, 9, 0))

library(huxtable)
huxTrans <- hux(dfTrans, add_colnames = TRUE) # column names become first row
huxTrans[1, 4] <- 'Combined Parameter Estimates' # get rid of the dots
align(huxTrans)[4:5, 1] <- 'right'
text_color(huxTrans)[c(3, 5), 1] <- 'blue'
text_color(huxTrans)[1, 3] <- 'blue'
italic(huxTrans)[1, c(1, 3)] <- TRUE

huxTrans # will automatically become LaTeX in RMarkdown
quick_pdf(huxTrans)

Which looks like this in the terminal:

RStudio terminal

And this in PDF output:

PDF

You can add borders as well if you want.

Upvotes: 3

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