geom_signif how to plot p-value labels on logarithmic y-axis

user_11197796 0
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Following the logic answered here I should be able to add p-value comparisons to the plot. Woudl really appreciate any help feedback as to what I'm doing wrong with my solution.

library(magrittr)
library(ggsignif)
library(ggpubr)

value<-c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.000273200055869626,
                 0, 0, 0, 0, 0, 0.000391899951754252, 7.79999691577276e-06, 0,
                 0, 0.000341800044604173, 0, 0.000160399989889521, 0, 0, 0.00014739991923847,
                 0, 0, 0.000200399960107021, 0, 0, 0, 0, 6.35000054462966e-05)
condition<-c("E","E","E","E","E","E","E","E","E","E","E","E","E",
                     "R","R","R","R","R","R","R","R","R","R","R","R","R",
                     "S","S","S","S","S","S","S","S","S","S","S")
species<-rep('B_theta',length(condition))
df <- data.frame(value,condition,species)

bact <- compare_means(value~condition, data = df,method = 't.test') %>%  
bact <- bact %>%  mutate(y_pos =  c(-3.5, -3.25, -3),labels = ifelse(p < 0.1, p.format, p.signif))
bact

.y. group1  group2  p   p.adj   p.format    p.signif    method  y_pos   labels
value   E   R   0.04859346  0.15    0.049   *           T-test  3.50    0.049
value   E   S   0.11168959  0.22    0.112   ns          T-test  3.25    ns
value   R   S   0.26876159  0.27    0.269   ns          T-test  3.00    ns

p <- ggboxplot(df, x = "condition", y = "value",
                  color = "condition", 
                  palette = "jco",add = "jitter")+
                  geom_signif(textsize=6, tip_length = 0.01, xmin=bact$group1,
                              xmax=bact$group2, annotations=bact$labels, y_position=bact$y_pos)+
                  scale_y_log10(limits=c(NA,0.001))+annotation_logticks(sides = "l")


Warning message:
"Transformation introduced infinite values in continuous y-axis"Warning message:
"Transformation introduced infinite values in continuous y-axis"Warning message:
"Transformation introduced infinite values in continuous y-axis"Warning message:
"Removed 29 rows containing non-finite values (stat_boxplot)."Warning message:
"Removed 29 rows containing non-finite values (stat_signif)."

enter image description here

ggpubr ggplot2 r
1 Answers

This is not an elegant solution and is not correct from a mathematical point of view. Anyway, here is the code. Zeros were arbitrarily set to 10^(-6). Maybe this trick can help you to reconsider the problem.

value <- c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.000273200055869626,
           0, 0, 0, 0, 0, 0.000391899951754252, 7.79999691577276e-06, 0,
           0, 0.000341800044604173, 0, 0.000160399989889521, 0, 0, 0.00014739991923847,
           0, 0, 0.000200399960107021, 0, 0, 0, 0, 6.35000054462966e-05)
condition <- c("E","E","E","E","E","E","E","E","E","E","E","E","E",
               "R","R","R","R","R","R","R","R","R","R","R","R","R",
               "S","S","S","S","S","S","S","S","S","S","S")
species <- rep('B_theta',length(condition))
df <- data.frame(value,condition,species)
    
bact <- compare_means(value~condition, data = df,method = 't.test')  
bact <- bact %>%  mutate(y_pos =  c(-3, -2.75, -2.5), 
                        labels = ifelse(p < 0.1, p.format, p.signif))

df$value[df$value==0] <- 10^(-6)
p <- ggboxplot(df, x = "condition", y = "value",
                  color = "condition", 
                  palette = "jco",add = "jitter")+
                  geom_signif(textsize=6, tip_length = 0.01, 
                              xmin=bact$group1, xmax=bact$group2, 
                              annotations=bact$labels, y_position=bact$y_pos)+
                  scale_y_continuous(trans = scales::log10_trans(), 
                                    breaks=10^c(-6,-5,-4,-3), 
                                    labels=c("0","1e-05","1e-04","1e-03")) +
                  annotation_logticks(sides = "l")
p

enter image description here

user_11666840
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