CODEWITHSUNDEEP
rggplot2annotations
Gabs Rossetti
Gabs Rossetti

Reputation: 31

geom_signif not showing all of the comparisons

I'm making line graphs from mean and SD summary data using ggplot.

I'm labelling significant differences using the geom_signif() function from the ggsignif package.

None of the comparisons between the two final points on the x axis (Day 2 and Day 3) are showing up on the plot. All of the other significance labelling is working fine.Why aren't these comparisons showing when all of the others are working fine?

I've copied the code for an example image and attached the plot it creates.

the plot it creates

I'm having the same problem with all of the plots in my panel figure.

panel figure

ortho_theme = theme(plot.title = element_text(face = "bold"),
                      axis.text.x = element_text(face = "bold", colour = "black", angle = 15, size = 12, hjust = 1),
                      axis.text.y = element_text( colour = "black", size = 12),
                      axis.title.y = element_text(face = "bold", colour = "black", size = 14),
                      legend.text = element_text(colour = "black", size = 12),
                      legend.title = element_text(face = "bold", colour = "black", size = 12))


(brain = 
  ggplot(Ortho_data, aes(x = Day, y = Cerebral_TOI_mean, group = factor(Condition), fill = factor(Condition))) +

   geom_errorbar(data = (Ortho_data %>% filter(Condition == "Stand")), 
                 aes(ymax = (Cerebral_TOI_mean),
                     ymin = (Cerebral_TOI_mean - Cerebral_TOI_SD)), width = 0.1) +  

   geom_errorbar(data = (Ortho_data %>% filter(Condition == "Supine")), 
                 aes(ymin = (Cerebral_TOI_mean),
                     ymax = (Cerebral_TOI_mean + Cerebral_TOI_SD)), width = 0.1) + 


   geom_line() + 
   geom_point(size = 4, shape = 21) +

  ggtitle("A") +
  ylab("Cerebral TOI (%)") + 
  xlab("") + 
  ylim(50, 85) +

  scale_fill_manual(values = c("black", "grey"), name = "Condition")+
  theme_classic() + 
  ortho_theme +

   annotate("text", x = 0.935, y = 78.6, label = "*", hjust = 0, size = 5) +

   geom_signif(comparisons = list(c("Sea level", "Day 2")), annotation = "‡", y_position = 82, vjust = -0.3, textsize = 3,
               tip_length = c(0.1, 0.02))+
   geom_signif(comparisons = list(c("Day 1", "Day 2")), annotation = "‡", y_position = 70, colour = "black", vjust = -0.3, textsize = 3,
               tip_length = c(0.1, 0.02))+
   geom_signif(comparisons = list(c("Day 1", "Day 3")), annotation = "‡", y_position = 75, colour = "black", vjust = -0.3, textsize = 3,
               tip_length = c(0.05, 0.2))+
   geom_signif(comparisons = list(c("Day 2", "Day 3")), annotation = "‡", y_position = 70, colour = "black", vjust = -0.3, textsize = 3)

  )

Upvotes: 2

Views: 3361

Answers (1)

Gabs Rossetti
Gabs Rossetti

Reputation: 31

I have solved this by moving the group aesthetic from the ggplot aes to the geom_line aes, as in the minimally reproducible example below.

This resolves the issue, but I don't understand why...

library(ggplot2)
library(ggsignif)

data = data.frame(Day = factor(c("Sea level", "Day 1", "Day 2", "Day 3", "Sea level", "Day 1", "Day 2", "Day 3"),
                               levels = c("Sea level", "Day 1", "Day 2", "Day 3")), 
                  Condition = c("Supine", "Supine", "Supine", "Supine", "Stand", "Stand", "Stand", "Stand"),          
                  Values = c(1,1,2,4,2,2,3,5))



ggplot(data, aes(x = Day, y = Values)) + 

   geom_line(aes(group = Condition)) + 
   geom_point()+

   geom_signif(comparisons = list(c("Day 2", "Day 3")), annotation = "‡")

Upvotes: 1

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