I want to interpret LaTeX formulas contained in a column of a dataset used to plot observations. The easiest way I found to do so is to use the TeX() function from {latex2exp} passed on to the labels argument of the scale_y_discrete() from {ggplot2}.
library(tibble)
library(ggplot2)
df <- tibble(x = c(1,2,3), y = c("Some text $A \\leq 2$", "$A = 2$", "$A \\geq 2$"))
ggplot(data = df, mapping = aes(x = x, y = y)) +
geom_bar(stat = "identity") +
scale_y_discrete(labels = function(labels) latex2exp::TeX(labels))
font_size <- 20
font_family <- "serif"
#' Theme for ggplot2
#'
#' @param ... Arguments passed to the theme function.
#' @export
#' @importFrom ggplot2 element_rect element_text element_blank element_line unit
#' rel theme
#'
theme_paper <- function (...) {
theme(
text = element_text(family = font_family),
plot.background = element_rect(fill = "transparent", color = NA),
panel.background = element_rect(fill = "transparent", color = NA),
# panel.border = element_rect(fill = NA, colour = "black", linewidth = 1),
panel.border = element_blank(),
axis.line = element_line(color = "black"),
axis.text = element_text(color = "black"),
axis.title = element_text(color = "black", size = rel(.8)),
legend.text = element_text(size = rel(1)),
legend.title = element_text(size = rel(1)),
legend.background = element_rect(fill = "transparent", color = NULL),
# legend.position = "bottom",
# legend.direction = "horizontal",
# legend.box = "vertical",
legend.key = element_blank(),
panel.spacing = unit(1, "lines"),
panel.grid.major = element_line(colour = "grey90"),
panel.grid.minor = element_blank(),
plot.title = element_text(hjust = 0, size = rel(.8), face = "bold"),
plot.title.position = "plot",
plot.margin = unit(c(1, 1, 1, 1), "lines"),
strip.background = element_rect(fill = NA, colour = NA),
strip.text = element_text(size = rel(.8))
)
}
theme_ggtern_paper <- function(...) {
font_family <- "CMU Serif"
font_size <- 20
theme(
strip.background = element_rect(colour = "black", fill = NA),
strip.text.x = element_text(colour = "black"),
strip.text = ggtext::element_markdown(),
text = element_text(family = font_family, size = unit(font_size, "pt")),
axis.title = element_text(size = rel(.8)),
tern.axis.arrow.show = TRUE,
tern.axis.arrow.sep = .13,
tern.axis.vshift = .05,
panel.border = element_rect(colour = NA)
)
}
#' From plot created with {tikzDevice}, create a standalone latex document
#' and compile it with pdflatex to save the plot as pdf
#'
#' @param filename Name of the tex file (WITHOUT THE EXTENSION) that contains
#' the tikzpicture.
#' @param path_to_latex Path to LaTeX engine (Defaults to
#' `/Library/TeX/texbin/`).
#' @param interpreter By default, use pdflatex (`pdflatex`).
#' @param path Path to the destination folder.
#' @param keep_tex should the tex file (only the one from the standalone doc)
#' be kept after compilation? Defaults to `FALSE`.
#' @param verbose A logical value indicating whether diagnostic messages are
#' printed when measuring dimensions of strings. Defaults to `FALSE`.
#' @param ignore.stdout A logical (not NA) indicating whether messages written
#' to ‘stdout’ should be ignored. Defaults to `TRUE`.
#' @param crop If `TRUE` (default to `FALSE`), the PDF is cropped using pdfcrop.
#'
plot_to_pdf <- function(filename,
path_to_latex = "/Library/TeX/texbin/",
interpreter = "pdflatex",
path = "./",
keep_tex = FALSE,
verbose = FALSE,
ignore.stdout = TRUE,
crop = FALSE) {
content <- paste0(
"\\documentclass{standalone}
\\usepackage{amsmath,amssymb,amsthm,mathtools,graphicx}
\\usepackage{array,dcolumn}
\\usepackage{tikz}
\\usetikzlibrary{arrows.meta, positioning, calc}
%\\usepackage{dsfont}
%\\usepackage{fontspec}
\\renewcommand{\\familydefault}{\\rmdefault}
%\\usepackage{natbib}
\\usepackage{microtype}
%\\usepackage{newtxtext,newtxmath}
%\\usepackage{times,mathpazo}
\\usepackage{pgfplots}
\\usetikzlibrary{pgfplots.groupplots}
\\usepackage{xcolor}
\\begin{document}
\\input{",
path, filename,
".tex}
\\end{document}"
)
# The file which will import the graph in tex format
fileConn <- file(paste0(path, filename, "_tmp.tex"))
writeLines(content, fileConn)
close(fileConn)
# Process tex file to get the PDF
system(
paste0(
path_to_latex,
interpreter, " -shell-escape -synctex=1 -interaction=nonstopmode ",
path,
filename, "_tmp.tex"),
ignore.stdout = TRUE
)
if (crop == TRUE) {
system(
paste0(
"pdfcrop ", filename, "_tmp.pdf ", filename, "_tmp.pdf"
)
)
}
if(!path %in% c(".", "./", "/"))
system(paste0("mv ", filename, "_tmp.pdf ", path))
system(paste0("rm ", filename, "_tmp.aux"))
system(paste0("rm ", filename, "_tmp.log"))
system(paste0("rm ", filename, "_tmp.synctex.gz"))
if (!keep_tex) {
system(paste0("rm ", path, filename, "_tmp.tex"))
}
system(paste0("mv ", path, filename, "_tmp.pdf ", path, filename, ".pdf"))
}
#' Save a ggplot2 plot as PDF, using LaTeX tikz
#'
#' @param plot A ggplot2 object.
#' @param path_to_latex Path to LaTeX engine (Defaults to
#' `/Library/TeX/texbin/`).
#' @param interpreter By default, use pdflatex (`pdflatex`).
#' @param path Path to the destination folder.
#' @param filename File name (without the extension).
#' @param keep_tex should the tex file be kept after compilation? Defaults to
#' `FALSE`.
#' @param width Width in inches (default to 15).
#' @param height Height in inches (default to 15).
#' @param verbose A logical value indicating whether diagnostic messages are
#' printed when measuring dimensions of strings. Defaults to `FALSE`.
#' @param ignore.stdout A logical (not NA) indicating whether messages written
#' to ‘stdout’ should be ignored. Defaults to `TRUE`.
#' @param crop If `TRUE` (default to `FALSE`), the PDF is cropped using pdfcrop.
#'
#' @importFrom tikzDevice tikz
#' @importFrom grDevices dev.off
#' @export
#' @md
#'
ggplot2_to_pdf <- function(plot,
path_to_latex = "/Library/TeX/texbin/",
interpreter = "pdflatex",
path = "./",
filename,
keep_tex = FALSE,
width = 15,
height = 15,
verbose = FALSE,
ignore.stdout = TRUE,
crop = FALSE) {
content <- paste0(
"\\documentclass{standalone}
\\usepackage{amsmath,amssymb,amsthm,mathtools,graphicx}
\\usepackage{array,dcolumn}
%\\usepackage{dsfont}
%\\usepackage{fontspec}
%\\setmainfont{Noto Sans}
%
\\usepackage{tikz}
\\usetikzlibrary{arrows.meta, positioning, calc}
\\usepackage{nicefrac}
%\\usepackage{natbib}
\\usepackage{microtype}
%\\usepackage{newtxtext,newtxmath}
%\\usepackage{times,mathpazo}
\\usepackage{pgfplots}
\\usetikzlibrary{pgfplots.groupplots}
\\usepackage{xcolor}
\\renewcommand{\\familydefault}{\\rmdefault}
\\begin{document}
\\input{",
path, filename,
"_content.tex}
\\end{document}"
)
# The file which will import the graph in tex format
fileConn <- file(paste0(path, filename, ".tex"))
writeLines(content, fileConn)
close(fileConn)
# Export graph to tex
tikz(file = paste0(
path,
filename, "_content.tex"),
width = width,
height = height,
verbose = verbose
)
print(plot)
dev.off()
# Move the scale from ggplot, if any
name_scale <- paste0(filename, "_content_ras1.png")
scale_exists <- file.exists(name_scale)
if (scale_exists & ! path %in% c(".", "./", "/")) {
system(paste0("mv ", name_scale, " ", path))
}
# Process tex file to get the PDF
system(
paste0(
path_to_latex,
interpreter, " -shell-escape -synctex=1 -interaction=nonstopmode ",
path,
filename, ".tex"),
ignore.stdout = TRUE
)
if (crop == TRUE) {
system(paste0("pdfcrop ", path, filename, ".pdf ", path, filename, ".pdf"))
}
if(!path %in% c(".", "./", "/")) system(paste0("mv ", filename, ".pdf ", path))
system(paste0("rm ", filename, ".aux"))
system(paste0("rm ", filename, ".log"))
system(paste0("rm ", filename, ".synctex.gz"))
if (!keep_tex) {
system(paste0("rm ", path, filename, ".tex"))
system(paste0("rm ", path, filename, "_content.tex"))
}
if (scale_exists) system(paste0("rm ", path, "/", name_scale))
}Example:
library(tikzDevice)
library(ggplot2)
p <- ggplot(data = iris, mapping = aes(x = Sepal.Length, y = Sepal.Width)) +
geom_point(mapping = aes(colour = Species)) +
theme_paper()
ggplot2_to_pdf(
plot = p, path = "./figs/", filename = "iris_ggplot2",
width = 5, height = 4
)