Hello,

I am using below code for box plot with geom significance but getting plot without adding significance value? I am interested to add geom significance value based on region.

My data structure is like this:

'data.frame':   54 obs. of  14 variables:
 $ SampleType  : Factor w/ 6 levels "2W_B_1Ash","2W_B_2Farm",..: 4 5 6 4 5 6 4 5 6 4 ...
 $ Region      : Factor w/ 2 levels "Barind","Madhupur": 2 2 2 2 2 2 2 2 2 2 ...
 $ Village_site: Factor w/ 18 levels "Bandiya","Bogajan",..: 18 18 18 12 12 12 1 1 1 2 ...
 $ Season      : Factor w/ 1 level "2W": 1 1 1 1 1 1 1 1 1 1 ...
 $ Treatment   : Factor w/ 3 levels "Ash","AshPlusFarmerPractise",..: 1 3 2 1 3 2 1 3 2 1 ...
 $ S_Mn        : num  365 363 366 389 369 ...
 $ S_Ni        : num  20.2 18.9 21 19.3 25.6 ...
 $ S_P         : num  445 435 505 318 381 ...
 $ S_Rb        : num  102.7 99.7 98.9 94 97.1 ...
 $ S_S         : num  191 187 191 129 171 ...
 $ S_Si        : num  302667 302333 301333 293333 301667 ...
 $ S_Sr        : num  123 123 122 147 143 ...
 $ S_Zn        : num  73.5 77.7 80.5 77.7 79.9 ...
 $ pH          : num  5.24 4.76 5.3 6.72 5.44 6.29 4.41 4.95 4.69 5.08 ...


library(reshape2)
library(ggplot2)
library(multcompView)
library(tidyverse)
library(ggsignif)
library(ggpubr)
list.files()

bpdata <- read.table("Soil1.chemical.txt", sep="\t", header=TRUE)
dput(bpdata)
str(bpdata)

bpdata[,"SampleType"] <- as.factor(bpdata[,"SampleType"])
bpdata <- cbind(row.names(bpdata),bpdata)
names(bpdata)[1] <- "sample"
#create paired comparison for box plots

bpdata$Region <- factor (bpdata$Region, levels = c("Madhupur", "Barind"))

cmpr <- list(c("Madhupur","Barind"))



data <- melt(bpdata, id = 1:6,variable.name="name")




v_factor_levels <- c("2W_B_1Ash", "2W_B_2Farm", "2W_B_3AshFarm", "2W_M_1Ash", "2W_M_2Farm", "2W_M_3AshFarm")





data$SampleType <- factor (data$SampleType, levels = v_factor_levels)


#df.m <- melt(bpdata, id.var = "SampleType")
library(ggsignif)
pdf("soil1.plot.pdf", width = 18, height = 12)

ncol=3
p <- ggplot(data = data, aes(x=SampleType, y=value,fill=SampleType)) +
theme_bw() +
theme(
      panel.grid.major=element_blank(),
      panel.grid.minor=element_blank(),
      plot.title = element_text(vjust = -8.5,hjust = 0.1),
      line=element_line(size=1),

      axis.text.x = element_text(size = 10, face ="bold", hjust = 0.5, colour = "black"),
      axis.text.y = element_text(size = 12, face ="bold", hjust = 0.5, colour = "black"),
      axis.ticks.x = element_blank()) +


theme(strip.background=element_rect(fill="white")) +
theme(strip.text=element_text(color="black",face="bold", size =14)) + 
geom_boxplot(aes(fill=SampleType),outlier.colour = NA) 
p + facet_wrap(.~name,scales="free_y", ncol = ncol) +  geom_signif(comparisons = cmpr,step_increase = 0.2,size=0.5,textsize=3,map_signif_level = T,tip_length = 0.1,test =t.test,margin_top = 0.1)


dev.off();

warning;

Warning messages:
1: Computation failed in `stat_signif()`:
missing value where TRUE/FALSE needed
2: Computation failed in `stat_signif()`:
missing value where TRUE/FALSE needed
3: Computation failed in `stat_signif()`:
missing value where TRUE/FALSE needed
4: Computation failed in `stat_signif()`:
missing value where TRUE/FALSE needed
5: Computation failed in `stat_signif()`:
missing value where TRUE/FALSE needed
6: Computation failed in `stat_signif()`:
missing value where TRUE/FALSE needed
7: Computation failed in `stat_signif()`:
missing value where TRUE/FALSE needed
8: Computation failed in `stat_signif()`:
missing value where TRUE/FALSE needed
9: Computation failed in `stat_signif()`:
missing value where TRUE/FALSE needed

Thanks