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I'm trying to get partially italicized facet headings in ggplot2. I want the facets in a specific order, which I specify using facet_grid(~factor(YSD, levels = c('465', '466', '1572')

Here's a head of my data

> head(df)
  YSD Media       OD Replicate
1 465 - Met 1.790500         1
2 465 - Met 1.616300         1
3 465 - Met 1.745700         1
4 465 - Met 2.439433         1
5 465 - Met 2.070033         1
6 465 - Met 2.192433         1

> dput(df[1:10,])
structure(list(
YSD = c("465", "465", "465", "465", "465", "465", "465", "465", "465", 
"465"), 
Media = c("- Met", "- Met", "- Met", "- Met", "- Met", "- Met", "30 µM 
Met", "30 µM Met", "30 µM Met", "30 µM Met"), 
OD = c(1.7905, 1.6163, 1.7457, 2.439433, 2.070033, 2.192433, 1.9288, 
1.5506, 1.5966, 2.204833), 
Replicate = c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L)), 
row.names = c(NA, 10L), 
class = "data.frame")

And here's my code:

df <- read.csv("37C all.txt", sep="\t", check.names=FALSE)
cbPalette <- c("#999999", "#E69F00", "#56B4E9", "#009E73", "#F0E442", "#0072B2", "#D55E00", "#CC79A7")

my_labels <- c(expression(paste(italic("C. glabrata"), "CBS138")),
           expression(paste(italic("C. glabrata "), Delta, "HTL")),
           expression(paste(italic("Met3p-Hsp90"))))

df$YSD <- as.character(df$YSD)

dplot <- ggplot(data = df, aes(x = Media, y = OD, fill = YSD)) +
geom_boxplot(outlier.colour = "white") +
geom_dotplot(binaxis='y', stackdir='center', dotsize=0.5, binwidth = NULL) +
facet_grid(~factor(YSD, levels = c('465', '466', '1572'), labels = my_labels)) +
scale_y_continuous(limits = c(0, 3.0)) +
scale_x_discrete(limits=c("- Met", "30 µM Met", "40 µM Met", "DMSO", "50 µM Radicicol")) +
theme(axis.text = element_text(size=12), axis.title = element_text(size=12)) +
theme_bw() +
theme(axis.text.x = element_text(angle = 80, vjust = 0.5)) +
theme(legend.position = "none") + 
labs(title = "37°C Adhesion")

This gives me this plot: plot

I've tried setting the levels externally like here and here using:

levels(df$YSD) = c("465" = expression(paste(italic("C. glabrata"), "CBS138")),
                    "466" = expression(paste(italic("C. glabrata "), Delta, "HTL")),
                    "1572" = expression(paste(italic("Met3p-Hsp90"))))

but I get the error message:

Error in levels(df$YSD) = c(`465` = expression(paste(italic("C. glabrata"),  : 
  unimplemented type 'expression' in 'HashTableSetup'

Any help would be hugely appreciated. Thank you.

jcrunden
  • 11
  • 3
  • Have a look at https://github.com/richardjtelford/ggpalaeo/blob/master/R/species_to_latin.R which deals with a similar problem – Richard Telford May 14 '21 at 21:34
  • Please share sample of data, e.g. the output of `dput(df)` or if that's too long, `dput(df[1:10,])`. Otherwise we each have to try our best to make data like yours to test out solutions, without knowing if it really is like yours. – Jon Spring May 14 '21 at 22:42
  • I've edited my original post to show a sample of my data. @RichardTelford, Would your species italiciser pick up the name of the third facet, which isn't a species name? – jcrunden May 15 '21 at 10:06

0 Answers0