All ggplot graphs grey even after adding color

Question

I recently updated R and ggplot2 to the versions (4.1.1 and 3.3.5 respectively). I was using this code to create plots in ggplot:

rejA<-c(0.05,0.10,0.00,0.05)
Tr<-c("Corn\nmale\nx\nCorn\nfemale","Corn\nmale\nx\nWheat\nfemale","Wheat\nmale\nx\nCorn\nfemale","Wheat\nmale\nx\nWheat\nfemale")
Matingdiet<-c("Same diet","Different diets","Different diets", "Same diet")
d<-as.data.frame(cbind(Tr,rejA,Matingdiet))
d$rejA<-as.numeric(as.character(d$rejA))
d$Matingdiet<-factor(d$Matingdiet,levels = rev(levels(d$Matingdiet)))

mycol<-RColorBrewer::brewer.pal(9,"YlOrBr")[c(7,4)]

dev.new()

pl<-ggplot(data = d, aes(x=Tr, y=rejA))+
  geom_col(aes( fill=Matingdiet))+
  labs(x = "Mating pairs",fill="Male and female from", y = "Proportion of mates rejected")+
  scale_y_continuous(limits=c(0,1),expand = c(0,0))+ 
  scale_fill_manual(values=mycol)+
  theme_bw() + 
  theme(panel.grid.major = element_blank(),
        panel.grid.minor = element_blank(), 
        axis.line.y = element_line(colour = "black"),
        axis.text=element_text(size = 10),
        strip.background = element_blank(),
        axis.text.y=element_text(size = 10),
        panel.border=element_blank(),
        panel.spacing.x = unit(1,"line"),
        strip.text.x = element_text(size = 20))+
  geom_hline(yintercept = 0)

pl

However, the colors are not showing up in the graph. I used the same code earlier to get this plot

However, now when I run the same code, all the bars are grey and there is no legend.

I have tried changing the colours in the code

pl<-ggplot(data = d, aes(x=Tr, y=rejA))+
   geom_col(aes( fill=Matingdiet))+
   labs(x = "Mating pairs",fill="Male and female from", y = "Proportion of mates rejected")+
   scale_y_continuous(limits=c(0,1),expand = c(0,0))+ 
   scale_fill_manual(values=c("red","blue"))+
   theme_bw() + 
   theme(panel.grid.major = element_blank(),
        panel.grid.minor = element_blank(), 
        axis.line.y = element_line(colour = "black"),
        axis.text=element_text(size = 10),
        strip.background = element_blank(),
        axis.text.y=element_text(size = 10),
        panel.border=element_blank(),
        panel.spacing.x = unit(1,"line"),
        strip.text.x = element_text(size = 20))+
   geom_hline(yintercept = 0)

   pl

This also return a graph with all bars in grey. I am not sure what to try now, especially since it was working earlier (in R version 3.5).

Answer 1

I'm not sure but in line

d$Matingdiet<-factor(d$Matingdiet,levels = rev(levels(d$Matingdiet)))

change data d from

                             Tr rejA      Matingdiet
1   Corn\nmale\nx\nCorn\nfemale 0.05       Same diet
2  Corn\nmale\nx\nWheat\nfemale 0.10 Different diets
3  Wheat\nmale\nx\nCorn\nfemale 0.00 Different diets
4 Wheat\nmale\nx\nWheat\nfemale 0.05       Same diet

to

                             Tr rejA Matingdiet
1   Corn\nmale\nx\nCorn\nfemale 0.05       <NA>
2  Corn\nmale\nx\nWheat\nfemale 0.10       <NA>
3  Wheat\nmale\nx\nCorn\nfemale 0.00       <NA>
4 Wheat\nmale\nx\nWheat\nfemale 0.05       <NA>

You're filling chart with NAs. Problem is by levels(d$Matingdiet), that Matingdiet is not yet an factor so it does not have any levels. I'm not sure about your purpose, but try add d$Matingdiet <- factor(d$Matingdiet) first then d$Matingdiet<-factor(d$Matingdiet,levels = rev(levels(d$Matingdiet))) will not cause any problems.