Greek letters disappear from pdf when exporting figure from R

Hi-

I am interested in generating a figure with a ∆ in the title of the y-axis. Basically, if I export the plot as a .png file it gives me the right symbol in the y-axis label, BUT if I export as a .pdf, the ∆ just turns into ".." Here is my code and data:

sp <- ggplot(qdata, mapping=aes(x=Time, y=delCt, color=Genotype))+ 
  geom_point(alpha=0.5)+
  geom_smooth(se=FALSE, size=0.5)+
  facet_grid(Gene~Species, scales="free_y")+
  scale_x_continuous(breaks=c(-12, 0, 6, 12))+
  labs(y="Relative expression (\u0394Ct)", x="Extended darkness (hours)")+
  theme_classic()+
  theme(axis.title=element_text(size=6, color="black"),
        axis.text=element_text(size=6, color="black"),
        strip.text=element_text(size=6, color="black", face="italic"),
        panel.border=element_rect(fill = NA, color="black"),
        legend.title=element_blank(),
        legend.text=element_text(size=6, color="black"),
        legend.position=c(0.30,0.67))+
  scale_color_manual(values=c("red", "black"))+
  scale_fill_manual(values=c("red", "black"))
sp

And the data:

> dput(qdata)
structure(list(Species = structure(c(1L, 1L, 1L, 1L, 1L, 1L, 
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 
1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 3L, 3L, 3L, 3L, 3L, 3L, 
3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 
3L, 3L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 
4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 5L, 5L, 5L, 5L, 5L, 5L, 
5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 
5L, 5L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 
2L, 2L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 
3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 4L, 4L, 4L, 4L, 4L, 4L, 
4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 
4L, 4L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 
5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 1L, 1L, 1L, 1L, 1L, 1L, 
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 
1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 3L, 3L, 3L, 3L, 3L, 3L, 
3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 
3L, 3L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 
4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 5L, 5L, 5L, 5L, 5L, 5L, 
5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 
5L, 5L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 
2L, 2L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 
3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 4L, 4L, 4L, 4L, 4L, 4L, 
4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 
4L, 4L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 
5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 1L, 1L, 1L, 1L, 1L, 1L, 
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 
1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 3L, 3L, 3L, 3L, 3L, 3L, 
3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 
3L, 3L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 
4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 5L, 5L, 5L, 5L, 5L, 5L, 
5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 
5L, 5L), .Label = c("Arabidopsis", "Nicotiana", "Mesembryanthemum", 
"Lotus", "Pisum"), class = "factor"), Genotype = c("pgm", "pgm", 
"pgm", "pgm", "pgm", "pgm", "pgm", "pgm", "pgm", "pgm", "pgm", 
"pgm", "WT", "WT", "WT", "WT", "WT", "WT", "WT", "WT", "WT", 
"WT", "WT", "WT", "pgm", "pgm", "pgm", "pgm", "pgm", "pgm", "pgm", 
"pgm", "pgm", "pgm", "pgm", "pgm", "WT", "WT", "WT", "WT", "WT", 
"WT", "WT", "WT", "WT", "WT", "WT", "WT", "pgm", "pgm", "pgm", 
"pgm", "pgm", "pgm", "pgm", "pgm", "pgm", "pgm", "pgm", "pgm", 
"WT", "WT", "WT", "WT", "WT", "WT", "WT", "WT", "WT", "WT", "WT", 
"WT", "pgm", "pgm", "pgm", "pgm", "pgm", "pgm", "pgm", "pgm", 
"pgm", "pgm", "pgm", "pgm", "WT", "WT", "WT", "WT", "WT", "WT", 
"WT", "WT", "WT", "WT", "WT", "WT", "pgm", "pgm", "pgm", "pgm", 
"pgm", "pgm", "pgm", "pgm", "pgm", "pgm", "pgm", "pgm", "WT", 
"WT", "WT", "WT", "WT", "WT", "WT", "WT", "WT", "WT", "WT", "WT", 
"pgm", "pgm", "pgm", "pgm", "pgm", "pgm", "pgm", "pgm", "pgm", 
"pgm", "pgm", "pgm", "WT", "WT", "WT", "WT", "WT", "WT", "WT", 
"WT", "WT", "WT", "WT", "WT", "pgm", "pgm", "pgm", "pgm", "pgm", 
"pgm", "pgm", "pgm", "pgm", "pgm", "pgm", "pgm", "WT", "WT", 
"WT", "WT", "WT", "WT", "WT", "WT", "WT", "WT", "WT", "WT", "pgm", 
"pgm", "pgm", "pgm", "pgm", "pgm", "pgm", "pgm", "pgm", "pgm", 
"pgm", "pgm", "WT", "WT", "WT", "WT", "WT", "WT", "WT", "WT", 
"WT", "WT", "WT", "WT", "pgm", "pgm", "pgm", "pgm", "pgm", "pgm", 
"pgm", "pgm", "pgm", "pgm", "pgm", "pgm", "WT", "WT", "WT", "WT", 
"WT", "WT", "WT", "WT", "WT", "WT", "WT", "WT", "pgm", "pgm", 
"pgm", "pgm", "pgm", "pgm", "pgm", "pgm", "pgm", "pgm", "pgm", 
"pgm", "WT", "WT", "WT", "WT", "WT", "WT", "WT", "WT", "WT", 
"WT", "WT", "WT", "pgm", "pgm", "pgm", "pgm", "pgm", "pgm", "pgm", 
"pgm", "pgm", "pgm", "pgm", "pgm", "WT", "WT", "WT", "WT", "WT", 
"WT", "WT", "WT", "WT", "WT", "WT", "WT", "pgm", "pgm", "pgm", 
"pgm", "pgm", "pgm", "pgm", "pgm", "pgm", "pgm", "pgm", "pgm", 
"WT", "WT", "WT", "WT", "WT", "WT", "WT", "WT", "WT", "WT", "WT", 
"WT", "pgm", "pgm", "pgm", "pgm", "pgm", "pgm", "pgm", "pgm", 
"pgm", "pgm", "pgm", "pgm", "WT", "WT", "WT", "WT", "WT", "WT", 
"WT", "WT", "WT", "WT", "WT", "WT", "pgm", "pgm", "pgm", "pgm", 
"pgm", "pgm", "pgm", "pgm", "pgm", "pgm", "pgm", "pgm", "WT", 
"WT", "WT", "WT", "WT", "WT", "WT", "WT", "WT", "WT", "WT", "WT", 
"pgm", "pgm", "pgm", "pgm", "pgm", "pgm", "pgm", "pgm", "pgm", 
"pgm", "pgm", "pgm", "WT", "WT", "WT", "WT", "WT", "WT", "WT", 
"WT", "WT", "WT", "WT", "WT", "pgm", "pgm", "pgm", "pgm", "pgm", 
"pgm", "pgm", "pgm", "pgm", "pgm", "pgm", "pgm", "WT", "WT", 
"WT", "WT", "WT", "WT", "WT", "WT", "WT", "WT", "WT", "WT", "pgm", 
"pgm", "pgm", "pgm", "pgm", "pgm", "pgm", "pgm", "pgm", "pgm", 
"pgm", "pgm", "WT", "WT", "WT", "WT", "WT", "WT", "WT", "WT", 
"WT", "WT", "WT", "WT", "pgm", "pgm", "pgm", "pgm", "pgm", "pgm", 
"pgm", "pgm", "pgm", "pgm", "pgm", "pgm", "WT", "WT", "WT", "WT", 
"WT", "WT", "WT", "WT", "WT", "WT", "WT", "WT", "pgm", "pgm", 
"pgm", "pgm", "pgm", "pgm", "pgm", "pgm", "pgm", "pgm", "pgm", 
"pgm", "WT", "WT", "WT", "WT", "WT", "WT", "WT", "WT", "WT", 
"WT", "WT", "WT", "pgm", "pgm", "pgm", "pgm", "pgm", "pgm", "pgm", 
"pgm", "pgm", "pgm", "pgm", "pgm", "WT", "WT", "WT", "WT", "WT", 
"WT", "WT", "WT", "WT", "WT", "WT", "WT", "pgm", "pgm", "pgm", 
"pgm", "pgm", "pgm", "pgm", "pgm", "pgm", "pgm", "pgm", "pgm", 
"WT", "WT", "WT", "WT", "WT", "WT", "WT", "WT", "WT", "WT", "WT", 
"WT", "pgm", "pgm", "pgm", "pgm", "pgm", "pgm", "pgm", "pgm", 
"pgm", "pgm", "pgm", "pgm", "WT", "WT", "WT", "WT", "WT", "WT", 
"WT", "WT", "WT", "WT", "WT", "WT", "pgm", "pgm", "pgm", "pgm", 
"pgm", "pgm", "pgm", "pgm", "pgm", "pgm", "pgm", "pgm", "WT", 
"WT", "WT", "WT", "WT", "WT", "WT", "WT", "WT", "WT", "WT", "WT", 
"pgm", "pgm", "pgm", "pgm", "pgm", "pgm", "pgm", "pgm", "pgm", 
"pgm", "pgm", "pgm", "WT", "WT", "WT", "WT", "WT", "WT", "WT", 
"WT", "WT", "WT", "WT", "WT", "pgm", "pgm", "pgm", "pgm", "pgm", 
"pgm", "pgm", "pgm", "pgm", "pgm", "pgm", "pgm", "WT", "WT", 
"WT", "WT", "WT", "WT", "WT", "WT", "WT", "WT", "WT", "WT"), 
    Time = c(-12, -12, -12, 0, 0, 0, 6, 6, 6, 12, 12, 12, -12, 
    -12, -12, 0, 0, 0, 6, 6, 6, 12, 12, 12, -12, -12, -12, 0, 
    0, 0, 6, 6, 6, 12, 12, 12, -12, -12, -12, 0, 0, 0, 6, 6, 
    6, 12, 12, 12, -12, -12, -12, 0, 0, 0, 6, 6, 6, 12, 12, 12, 
    -12, -12, -12, 0, 0, 0, 6, 6, 6, 12, 12, 12, -12, -12, -12, 
    0, 0, 0, 6, 6, 6, 12, 12, 12, -12, -12, -12, 0, 0, 0, 6, 
    6, 6, 12, 12, 12, -12, -12, -12, 0, 0, 0, 6, 6, 6, 12, 12, 
    12, -12, -12, -12, 0, 0, 0, 6, 6, 6, 12, 12, 12, -12, -12, 
    -12, 0, 0, 0, 6, 6, 6, 12, 12, 12, -12, -12, -12, 0, 0, 0, 
    6, 6, 6, 12, 12, 12, -12, -12, -12, 0, 0, 0, 6, 6, 6, 12, 
    12, 12, -12, -12, -12, 0, 0, 0, 6, 6, 6, 12, 12, 12, -12, 
    -12, -12, 0, 0, 0, 6, 6, 6, 12, 12, 12, -12, -12, -12, 0, 
    0, 0, 6, 6, 6, 12, 12, 12, -12, -12, -12, 0, 0, 0, 6, 6, 
    6, 12, 12, 12, -12, -12, -12, 0, 0, 0, 6, 6, 6, 12, 12, 12, 
    -12, -12, -12, 0, 0, 0, 6, 6, 6, 12, 12, 12, -12, -12, -12, 
    0, 0, 0, 6, 6, 6, 12, 12, 12, -12, -12, -12, 0, 0, 0, 6, 
    6, 6, 12, 12, 12, -12, -12, -12, 0, 0, 0, 6, 6, 6, 12, 12, 
    12, -12, -12, -12, 0, 0, 0, 6, 6, 6, 12, 12, 12, -12, -12, 
    -12, 0, 0, 0, 6, 6, 6, 12, 12, 12, -12, -12, -12, 0, 0, 0, 
    6, 6, 6, 12, 12, 12, -12, -12, -12, 0, 0, 0, 6, 6, 6, 12, 
    12, 12, -12, -12, -12, 0, 0, 0, 6, 6, 6, 12, 12, 12, -12, 
    -12, -12, 0, 0, 0, 6, 6, 6, 12, 12, 12, -12, -12, -12, 0, 
    0, 0, 6, 6, 6, 12, 12, 12, -12, -12, -12, 0, 0, 0, 6, 6, 
    6, 12, 12, 12, -12, -12, -12, 0, 0, 0, 6, 6, 6, 12, 12, 12, 
    -12, -12, -12, 0, 0, 0, 6, 6, 6, 12, 12, 12, -12, -12, -12, 
    0, 0, 0, 6, 6, 6, 12, 12, 12, -12, -12, -12, 0, 0, 0, 6, 
    6, 6, 12, 12, 12, -12, -12, -12, 0, 0, 0, 6, 6, 6, 12, 12, 
    12, -12, -12, -12, 0, 0, 0, 6, 6, 6, 12, 12, 12, -12, -12, 
    -12, 0, 0, 0, 6, 6, 6, 12, 12, 12, -12, -12, -12, 0, 0, 0, 
    6, 6, 6, 12, 12, 12, -12, -12, -12, 0, 0, 0, 6, 6, 6, 12, 
    12, 12, -12, -12, -12, 0, 0, 0, 6, 6, 6, 12, 12, 12, -12, 
    -12, -12, 0, 0, 0, 6, 6, 6, 12, 12, 12, -12, -12, -12, 0, 
    0, 0, 6, 6, 6, 12, 12, 12, -12, -12, -12, 0, 0, 0, 6, 6, 
    6, 12, 12, 12, -12, -12, -12, 0, 0, 0, 6, 6, 6, 12, 12, 12, 
    -12, -12, -12, 0, 0, 0, 6, 6, 6, 12, 12, 12, -12, -12, -12, 
    0, 0, 0, 6, 6, 6, 12, 12, 12, -12, -12, -12, 0, 0, 0, 6, 
    6, 6, 12, 12, 12, -12, -12, -12, 0, 0, 0, 6, 6, 6, 12, 12, 
    12, -12, -12, -12, 0, 0, 0, 6, 6, 6, 12, 12, 12, -12, -12, 
    -12, 0, 0, 0, 6, 6, 6, 12, 12, 12), Gene = c("DIN6", "DIN6", 
    "DIN6", "DIN6", "DIN6", "DIN6", "DIN6", "DIN6", "DIN6", "DIN6", 
    "DIN6", "DIN6", "DIN6", "DIN6", "DIN6", "DIN6", "DIN6", "DIN6", 
    "DIN6", "DIN6", "DIN6", "DIN6", "DIN6", "DIN6", "DIN6", "DIN6", 
    "DIN6", "DIN6", "DIN6", "DIN6", "DIN6", "DIN6", "DIN6", "DIN6", 
    "DIN6", "DIN6", "DIN6", "DIN6", "DIN6", "DIN6", "DIN6", "DIN6", 
    "DIN6", "DIN6", "DIN6", "DIN6", "DIN6", "DIN6", "DIN6", "DIN6", 
    "DIN6", "DIN6", "DIN6", "DIN6", "DIN6", "DIN6", "DIN6", "DIN6", 
    "DIN6", "DIN6", "DIN6", "DIN6", "DIN6", "DIN6", "DIN6", "DIN6", 
    "DIN6", "DIN6", "DIN6", "DIN6", "DIN6", "DIN6", "DIN6", "DIN6", 
    "DIN6", "DIN6", "DIN6", "DIN6", "DIN6", "DIN6", "DIN6", "DIN6", 
    "DIN6", "DIN6", "DIN6", "DIN6", "DIN6", "DIN6", "DIN6", "DIN6", 
    "DIN6", "DIN6", "DIN6", "DIN6", "DIN6", "DIN6", "DIN6", "DIN6", 
    "DIN6", "DIN6", "DIN6", "DIN6", "DIN6", "DIN6", "DIN6", "DIN6", 
    "DIN6", "DIN6", "DIN6", "DIN6", "DIN6", "DIN6", "DIN6", "DIN6", 
    "DIN6", "DIN6", "DIN6", "DIN6", "DIN6", "DIN6", "BCAT2", 
    "BCAT2", "BCAT2", "BCAT2", "BCAT2", "BCAT2", "BCAT2", "BCAT2", 
    "BCAT2", "BCAT2", "BCAT2", "BCAT2", "BCAT2", "BCAT2", "BCAT2", 
    "BCAT2", "BCAT2", "BCAT2", "BCAT2", "BCAT2", "BCAT2", "BCAT2", 
    "BCAT2", "BCAT2", "BCAT2", "BCAT2", "BCAT2", "BCAT2", "BCAT2", 
    "BCAT2", "BCAT2", "BCAT2", "BCAT2", "BCAT2", "BCAT2", "BCAT2", 
    "BCAT2", "BCAT2", "BCAT2", "BCAT2", "BCAT2", "BCAT2", "BCAT2", 
    "BCAT2", "BCAT2", "BCAT2", "BCAT2", "BCAT2", "BCAT2", "BCAT2", 
    "BCAT2", "BCAT2", "BCAT2", "BCAT2", "BCAT2", "BCAT2", "BCAT2", 
    "BCAT2", "BCAT2", "BCAT2", "BCAT2", "BCAT2", "BCAT2", "BCAT2", 
    "BCAT2", "BCAT2", "BCAT2", "BCAT2", "BCAT2", "BCAT2", "BCAT2", 
    "BCAT2", "BCAT2", "BCAT2", "BCAT2", "BCAT2", "BCAT2", "BCAT2", 
    "BCAT2", "BCAT2", "BCAT2", "BCAT2", "BCAT2", "BCAT2", "BCAT2", 
    "BCAT2", "BCAT2", "BCAT2", "BCAT2", "BCAT2", "BCAT2", "BCAT2", 
    "BCAT2", "BCAT2", "BCAT2", "BCAT2", "BCAT2", "BCAT2", "BCAT2", 
    "BCAT2", "BCAT2", "BCAT2", "BCAT2", "BCAT2", "BCAT2", "BCAT2", 
    "BCAT2", "BCAT2", "BCAT2", "BCAT2", "BCAT2", "BCAT2", "BCAT2", 
    "BCAT2", "BCAT2", "BCAT2", "BCAT2", "BCAT2", "BCAT2", "BCAT2", 
    "KINy1", "KINy1", "KINy1", "KINy1", "KINy1", "KINy1", "KINy1", 
    "KINy1", "KINy1", "KINy1", "KINy1", "KINy1", "KINy1", "KINy1", 
    "KINy1", "KINy1", "KINy1", "KINy1", "KINy1", "KINy1", "KINy1", 
    "KINy1", "KINy1", "KINy1", "KINy1", "KINy1", "KINy1", "KINy1", 
    "KINy1", "KINy1", "KINy1", "KINy1", "KINy1", "KINy1", "KINy1", 
    "KINy1", "KINy1", "KINy1", "KINy1", "KINy1", "KINy1", "KINy1", 
    "KINy1", "KINy1", "KINy1", "KINy1", "KINy1", "KINy1", "KINy1", 
    "KINy1", "KINy1", "KINy1", "KINy1", "KINy1", "KINy1", "KINy1", 
    "KINy1", "KINy1", "KINy1", "KINy1", "KINy1", "KINy1", "KINy1", 
    "KINy1", "KINy1", "KINy1", "KINy1", "KINy1", "KINy1", "KINy1", 
    "KINy1", "KINy1", "KINy1", "KINy1", "KINy1", "KINy1", "KINy1", 
    "KINy1", "KINy1", "KINy1", "KINy1", "KINy1", "KINy1", "KINy1", 
    "KINy1", "KINy1", "KINy1", "KINy1", "KINy1", "KINy1", "KINy1", 
    "KINy1", "KINy1", "KINy1", "KINy1", "KINy1", "KINy1", "KINy1", 
    "KINy1", "KINy1", "KINy1", "KINy1", "KINy1", "KINy1", "KINy1", 
    "KINy1", "KINy1", "KINy1", "KINy1", "KINy1", "KINy1", "KINy1", 
    "KINy1", "KINy1", "KINy1", "KINy1", "KINy1", "KINy1", "KINy1", 
    "KINy1", "TPS9", "TPS9", "TPS9", "TPS9", "TPS9", "TPS9", 
    "TPS9", "TPS9", "TPS9", "TPS9", "TPS9", "TPS9", "TPS9", "TPS9", 
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    0.006301889, 0.004560265, 0.004955799, 0.065911164, 0.053536501, 
    0.037248686, 0.180491149, 0.283220971, 0.234338624, 0.282567347, 
    2.969047141, 0.224273852, 0.013446116, 0.02509134, 0.031906629, 
    0.184283652, 0.022302254, 0.157854431, 0.675174973, 0.726986259, 
    0.703846792, 0.377182157, 0.445449359, 0.279321785, 0.034434535, 
    0.067920929, 0.039100567, 0.068710132, 0.070641837, 0.059265377, 
    0.356836063, 0.402390086, 0.224792634, 0.382447423, 0.261823531, 
    0.317904792, 0.032955582, 0.028755864, 0.017098339, 0.420448208, 
    0.406126198, 0.49425701, 0.907519155, 1.01865581, 1.076737568, 
    1.245449623, 1.049716684, 1.079228237, 0.054283843, 0.052921582, 
    0.05440941, 0.090037304, 0.067920929, 0.067296098, 1.094293701, 
    0.983956654, 1.049716684, 1.433955248, 1.31646272, 1.328685814, 
    0.002919627, 0.001262063, 0.001397115, 0.007563834, 0.008509755, 
    0.00320232, 0.065304822, 0.062355761, 0.056198158, 0.20166044, 
    0.302149264, 0.264865774, 0.004721082, 0.003942519, 0.00390625, 
    0.003284752, 0.002820174, 0.00271155, 0.041044517, 0.043888902, 
    0.040292822, 0.326842312, 0.230046913, 0.267325, 0.234338624, 
    0.228457863, 0.156764051, 0.782773416, 0.700601833, 0.708742433, 
    0.939522749, 0.825496116, 0.890898718, 0.637280314, 0.687770909, 
    0.667419927, 0.419477887, 0.481853559, 0.529731547, 0.661280073, 
    0.686183655, 0.643197335, 0.968170696, 1.154018752, 1.180992661, 
    0.77916458, 0.810377861, 0.757858283, 0.001847769, 0.002031367, 
    0.00192179, 0.013856115, 0.017297012, 0.007255714, 0.021893807, 
    0.036906021, 0.059128603, 0.096054699, 0.108067154, 0.127921736, 
    0.00837323, 0.007357, 0.007172375, 0.011651558, 0.006524124, 
    0.00439476, 0.065759053, 0.095833022, 0.091929179, 0.10438599, 
    4.542017715, 0.075015542, 0.030115847, 0.038207509, 0.028822381, 
    0.074325445, 0.081146162, 0.0838139, 0.530956902, 0.526072424, 
    0.517632462, 0.366868091, 0.429282718, 0.340721919, 0.05685115, 
    0.052677597, 0.042003887, 0.079476198, 0.069830446, 0.074842419, 
    0.465439858, 0.443395695, 0.398688344, 0.353553391, 0.346277367, 
    0.339151082, 0.009843133, 0.007476956, 0.003150944, 0.041044517, 
    0.026156863, 0.060092691, 0.182588356, 0.142266379, 0.1261606, 
    0.105598897, 0.102237757, 0.154963462, 0.010404369, 0.011705524, 
    0.007222263, 0.01248783, 0.008069342, 0.006419456, 0.109070536, 
    0.117169312, 0.077302917, 0.259414915, 0.227930622, 0.189902833, 
    0.005095125, 0.007546378, 0.006509068, 0.00464534, 0.00485381, 
    0.002787782, 0.006928058, 0.013856115, 0.01558894, 0.076946526, 
    0.063665988, 0.040761002, 0.008334627, 0.004507886, 0.003997554, 
    0.006157953, 0.003997554, 0.002207557, 0.008748997, 0.01092164, 
    0.018156962, 0.054661417, 0.056589048, 0.070478808, 0.046391362, 
    0.060371021, 0.046391362, 0.031177881, 0.028099079, 0.031322286, 
    0.052072543, 0.044194174, 0.050883204, 0.066063628, 0.040199833, 
    0.063665988, 0.104145086, 0.079476198, 0.067920929, 0.048249796, 
    0.044501569, 0.055296552, 0.073471744, 0.092354965, 0.112656308, 
    0.069991975, 0.092141826, 0.092568597)), row.names = c(NA, 
-600L), spec = structure(list(cols = list(Species = structure(list(), class = c("collector_character", 
"collector")), Genotype = structure(list(), class = c("collector_character", 
"collector")), Time = structure(list(), class = c("collector_double", 
"collector")), Gene = structure(list(), class = c("collector_character", 
"collector")), delCt = structure(list(), class = c("collector_double", 
"collector")), Expression = structure(list(), class = c("collector_double", 
"collector"))), default = structure(list(), class = c("collector_guess", 
"collector")), skip = 1), class = "col_spec"), class = c("spec_tbl_df", 
"tbl_df", "tbl", "data.frame"))

Thanks,

Erik

Hi @Soulhog,
I was able to replicate the error you came across. One workaround for the character not printing is that you can take advantage of ggplot's ability to parse plotmath expressions.

labs(y=expression("Relative expression ("*Delta*"Ct)")), 
   x="Extended darkness (hours)")

with saving the plot using ggsave.

giving:sp.pdf (56.0 KB) (At least on a mac).

1 Like

Hi @Soulhog,
There's two steps involved here. The first is transforming qdata$Gene into properly formatted character format, so just one pair of opening and closing quotes:

library("plyr")
qdata3 <- transform(qdata, Gene = revalue(Gene, c("KINy1" = "KIN*gamma*1")))

The reason why it worked in the first example was that *Delta* was passed as an argument into labs(y = expression()).

The second step is specifying that you want to parse the embedded plotmath in the facet labels :

facet_grid(Gene ~ Species, scales = "free_y", labeller = label_parsed) + ...
1 Like

Good catch. In this version, we can use the italicized formatting
in the plotmath expressions, and use label_parsed as before. I'm assuming that you don't want *gamma* to be italicized.

library("plyr")
library("ggplot2")

make_italic <- function(x){
  x <- paste0("italic('", x, "')")
}

# Convert levels to use italic formatting in plotmath
qdata3 <- transform(qdata, Gene = make_italic(Gene),
  Species = make_italic(Species))

# Fix the case for KIN*gamma*1
qdata3 <- transform(qdata3,Gene = revalue(Gene,
  c("italic('KINy1')" = "italic('KIN'*gamma*'1')")))

# Still use label_parsed, but now it will process italics as well

sp <- ggplot(qdata3, mapping=aes(x=Time, y=delCt, color=Genotype))+ 
  geom_point(alpha=0.5)+
  geom_smooth(se=FALSE, size=0.5)+
  facet_grid(Gene ~ Species, scales = "free_y",
    labeller = label_parsed) +
  scale_x_continuous(breaks=c(-12, 0, 6, 12))+
  labs(y=expression("Relative expression ("*Delta*"Ct)"), 
   x="Extended darkness (hours)") +
  theme_classic()+
  theme(axis.title=element_text(size=6, color="black"),
        axis.text=element_text(size=6, color="black"),
        strip.text=element_text(size=6, color="black"), # Remove italics
        panel.border=element_rect(fill = NA, color="black"),
        legend.title=element_blank(),
        legend.text=element_text(size=6, color="black"),
        legend.position=c(0.30,0.67))+
  scale_color_manual(values=c("red", "black"))+
  scale_fill_manual(values=c("red", "black"))

sp
1 Like

Hi @jrmuirhead

OK sorry for the double-up on the issues, but I didn't want to wait for you to get back to me. I have another issue. I am putting overlaying stars on the figure with geom_text(), here is the data and code:

DATA

> dput(labeldata)
structure(list(Species = structure(c(1L, 1L, 1L, 2L, 2L, 2L, 
2L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 4L, 4L, 4L, 4L, 5L, 5L, 5L, 5L, 
5L), .Label = c("Arabidopsis", "Nicotiana", "Mesembryanthemum", 
"Lotus", "Pisum"), class = "factor"), Genotype = c("WT", "WT", 
"WT", "WT", "WT", "WT", "WT", "WT", "WT", "WT", "WT", "WT", "WT", 
"WT", "WT", "WT", "WT", "WT", "WT", "WT", "WT", "WT", "WT"), 
    Time = c(0, 0, 0, -12, 0, -12, 0, 0, 0, 6, 0, 6, -12, 0, 
    0, -12, 0, -12, 6, 0, -12, 0, -12), Gene = c("BCAT2", "DIN6", 
    "KINy1", "ACX2", "DIN6", "DIN6", "KINy1", "ACX2", "DIN6", 
    "DIN6", "KINy1", "KINy1", "TPS9", "TPS9", "BCAT2", "KINy1", 
    "KINy1", "TPS9", "ACX2", "BCAT2", "KINy1", "KINy1", "TPS9"
    ), delCt = c(-3, 5, 1, -2, 4, -3, 1, -2, 2, 4, -1, 2, -1, 
    1, 0, -3, -2, -5, -2, 1, -2, 0, 1)), row.names = c(NA, -23L
), spec = structure(list(cols = list(Species = structure(list(), class = c("collector_character", 
"collector")), Genotype = structure(list(), class = c("collector_character", 
"collector")), Time = structure(list(), class = c("collector_double", 
"collector")), Gene = structure(list(), class = c("collector_character", 
"collector")), delCt = structure(list(), class = c("collector_double", 
"collector"))), default = structure(list(), class = c("collector_guess", 
"collector")), skip = 1), class = "col_spec"), class = c("spec_tbl_df", 
"tbl_df", "tbl", "data.frame"))

code:

using sp from the first message as the name of the plot:

gene_expression <- sp + geom_text(data=labeldata, label="*", show.legend=FALSE, size=3)
gene_expression

When I run that code, something very strange happens. It doubles each level of the factor... so I ran it through the same steps as with the other data:

labeldata3 <- transform(labeldata, Gene = make_italic(Gene), Species=make_italic(Species))
labeldata3 <- transform(labeldata3,Gene = revalue(Gene, c("italic('KINy1')" = "italic('KIN'*gamma*'1')")))

and that fixed it, but now the levels are in the wrong order. I had initially ordered the levels using

qdata$Species <- factor(qdata$Species, levels=c("Arabidopsis", "Nicotiana", "Mesembryanthemum", "Lotus", "Pisum"))

labeldata$Species <- factor(labeldata$Species, levels=c("Arabidopsis", "Nicotiana", "Mesembryanthemum", "Lotus", "Pisum"))

But now they are in alphabetical order again!

Let me know if you need more information, and thanks for all your help so far!

Thanks,

Erik

Hi @Soulhog,
To get the levels of the species in the order, we can change the make_italic function above to return a factor:

make_italic <- function(x){
  x <- paste0("italic('", x, "')")
  x <- factor(x, levels = unique(x))
}
1 Like

Hi @Soulhog
Sorry, I tried but ended up stumped wrt to italicizing plotmath greek letters.

That's OK, I don't think it's essential that the greek letter is italicized. If you end up figuring it out, I would love to know, though.

This package may help:
https://cran.r-project.org/web/packages/ggtext/index.html

This topic was automatically closed 7 days after the last reply. New replies are no longer allowed.

Thank you so much!

I have another problem, though. I would also like to re-name one of the levels of the qdata$Gene variable also using greek lettering. Here is my code:

qdata2 <- transform(qdata, Gene=revalue(Gene,c("KINy1"="KIN\u03b31")))

I run into the same problem as before, where the .pdf file contains ".." instead of the gamma.

so I tried the same way as with the other example:

qdata3 <- transform(qdata, Gene=revalue(Gene,c("KINy1"="KIN"*gamma*"1")))

but it gave me this error message:

Error in "KIN" * gamma : non-numeric argument to binary operator
In addition: Warning messages:
1: In grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'KINγ1' in 'mbcsToSbcs': dot substituted for <ce>
2: In grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'KINγ1' in 'mbcsToSbcs': dot substituted for <b3>
3: In grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'KINγ1' in 'mbcsToSbcs': dot substituted for <ce>
4: In grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'KINγ1' in 'mbcsToSbcs': dot substituted for <b3>

Just so we are clear, I would like to have the lower case gamma, so that the level is changed from "KINy1" to "KINgamma1"

Thanks,

Erik

Hi @jrmuirhead,

Thanks again. We are almost there. Your code worked well, however, now the vertical facet labels are no longer italic. In the original code for the figure, I have a theme() command:

strip.text=element_text(size=6, color="black", face="italic")

because I want both of the facet labels to be italic face.

It looks like the labeller=label_parsed command may have overriden the strip.text command?

Thanks,

Erik

OK, thanks. And if I wanted to have the gamma also be italicized, how would I write that code?