knitr: cannot create a figure with utf-8 character - r

Question

The following is my .Rnw file:
\documentclass{article}
\begin{document}
<<myChunk>>=
options(warn = 2)
library(ggplot2)
library(directlabels)
data(BodyWeight,package="nlme")
BodyWeight$temp <- as.character(BodyWeight$Rat)
BodyWeight$temp[BodyWeight$temp == "4"] <- "HI₂"
p <- qplot(Time,weight,data=BodyWeight,colour=temp,geom="line")
direct.label(p,"first.qp")
#
\end{document}
The following is how I call knitr from R:
library(knitr)
# I have tryied this but doesn't make difference:
# pdf.options(encoding='ISOLatin2.enc')
knit("mwe_knitr.Rnw")
I get following as output:
> knit("mwe_knitr.Rnw")
processing file: mwe_knitr.Rnw
|...................... | 33%
ordinary text without R code
|........................................... | 67%
label: myChunk
Quitting from lines 5-13 (mwe_knitr.Rnw)
Error in grid.Call(L_convert, x, as.integer(whatfrom), as.integer(whatto), :
(converted from warning) conversion failure on 'HI₂' in 'mbcsToSbcs': dot substituted for <e2>
I tried solutions with encoding, such as posted here:
Rhtml: Warning: conversion failure on '<var>' in 'mbcsToSbcs': dot substituted for <var>
(I note in comment above exactly where I try the solution to that problem) but it did not seem to change nothing for me.
I am using R 3.3.1 and knitr package 1.13 on Ubuntu.

Answer 1

It looks like using the cairo_pdf device resolves this issue. In the setup chunk below, I set the device option to the cairo_pdf device (that's the line that begins option(device = ...) and the global chunk option dev to default to "cairo_pdf" (in the line that begins knitr::opts_chunk$set(...). This approach is discussed in the knitr documentation (see the section Encoding of Multibyte Characters) and in Issue #436.
I've made a few other changes:
Instead of "hard-coding" "HI₂" I've used the Unicode symbol for the subscripted 2, "\U2082".
Changed the plot call to "standard" ggplot rather than qplot.
Changed from calling directlabels after making the plot to calling geom_dl to add direct labels within the "standard" ggplot workflow.
Set the fontfamily within geom_dl. I found that the subscript 2 was rendered with some font families, but not others.
Changed the warn option to zero (the default) so that warnings won't be turned into errors. I just did this while I was testing the code, but it can, of course, be set back to 2 if desired.
The chunk myChunk1a creates the plot. The chunk myChunk1b creates basically the same plot, but in multiple versions, each using a different font family. In these versions, you can see that the subscript 2 is rendered with some font families, but not others. I'm not sure what determines this and the results may be different on your system.
\documentclass{article}
\begin{document}
<<setup, include=FALSE>>=
options(warn = 0)
options(device = function(file, width = 7, height = 7, ...) {
cairo_pdf(tempfile(), width = width, height = height, ...)
})
knitr::opts_chunk$set(echo = FALSE, message=FALSE, warning=FALSE, dev="cairo_pdf")
#
<<myChunk>>=
library(ggplot2)
library(directlabels)
library(gridExtra)
library(dplyr)
data(BodyWeight,package="nlme")
BodyWeight$temp <- as.character(BodyWeight$Rat)
BodyWeight$temp[BodyWeight$temp=="4"] = "HI\U2082"
# Change first value so that HI2 label is easily visible
BodyWeight$weight[BodyWeight$temp=="HI\U2082" & BodyWeight$Time==1] = 350
#
<<myChunk1a, fig.height=5>>=
ggplot(BodyWeight, aes(Time, weight, colour=temp)) +
geom_line() +
geom_dl(method=list("first.qp", fontfamily="Helvetica", cex=1), aes(label=temp)) +
theme_bw() +
ggtitle("Helvetica") +
guides(colour=FALSE)
#
<<myChunk1b, fig.height=11>>=
# Create several plots, each demonstrating a different font family for the labels
grid.arrange(grobs=lapply(c("Helvetica","Courier","Palatino","Times","Serif"), function(f) {
ggplot(BodyWeight, aes(Time, weight, colour=temp)) +
geom_line() +
geom_dl(method=list("first.qp", fontfamily=f, cex=1), aes(label=temp)) +
labs(x="") +
theme_bw() +
theme(plot.margin=unit(c(0,0,0,0), "lines"),
text=element_text(size=9)) +
ggtitle(f) +
guides(colour=FALSE)
}), ncol=1)
#
<<myChunk2, fig.height=5>>=
data(BodyWeight,package="nlme")
BodyWeight$temp <- as.character(BodyWeight$Rat)
# Change first value so that HI2 label is easily visible
BodyWeight$weight[BodyWeight$temp=="4" & BodyWeight$Time==1] = 350
# Set temp==4 to desired expression
BodyWeight$temp[BodyWeight$temp == "4"] <- paste(expression(HI[2]))
# Convert temp to factor to set order
BodyWeight$temp = factor(BodyWeight$temp, levels=unique(BodyWeight$temp))
qplot(Time, weight, data=BodyWeight, colour=temp, geom="line") +
guides(colour=FALSE) +
geom_text(data=BodyWeight %>% group_by(temp) %>%
filter(Time == min(Time)),
aes(label=temp, x=Time-0.5, y=weight), parse=TRUE, hjust=1) +
theme_bw()
#
\end{document}
Here's what the plot from myChunk1a looks like: