Add errorbar and p-value on barplot with ggsignif

Creating informative and visually appealing barplots is essential for data analysis and presentation. In this blog post, we will demonstrate how to add error bars and p-values to barplots using the ggsignif package in R. This will help you highlight the statistical significance of your data in a clear and concise manner.

Prepare data

library(tidyverse)
library(here)
library(ggsignif)
library(ggh4x)
dfb <- read.csv(here("projects", "data", "221001_barplot.csv"), header = FALSE)
dfb
##                    V1   V2   V3   V4   V5   V6   V7 V8
## 1             Control 0.06 0.00 0.39 0.22 0.22 0.36 NA
## 2                  F5 0.99 1.00 0.95 0.97 0.97   NA NA
## 3 pAtUbi3:CDS-Rps11-1 1.00 0.67 0.94 1.00 1.00   NA NA
## 4 pAtUbi3:CDS-Rps11-2 0.94 1.00 0.94 0.94 1.00 1.00  1
dfb.1 <- dfb %>%
    pivot_longer(!V1) %>%
    select(V1, value) %>%
    na.omit()
dfb.1
## # A tibble: 23 × 2
##    V1      value
##    <chr>   <dbl>
##  1 Control  0.06
##  2 Control  0   
##  3 Control  0.39
##  4 Control  0.22
##  5 Control  0.22
##  6 Control  0.36
##  7 F5       0.99
##  8 F5       1   
##  9 F5       0.95
## 10 F5       0.97
## # ℹ 13 more rows

Define errorbar function

ebtop <- function(x) {
    return(mean(x) + sd(x) / sqrt(length(x)))
}
ebbottom <- function(x) {
    return(mean(x) - sd(x) / sqrt(length(x)))
}

Add errorbar and p-value

p <- ggplot(data = dfb.1, aes(x = V1, y = value)) +
    stat_summary(
        geom = "bar",
        fun = mean,
        fill = "#c6c3c3"
    ) +
    stat_summary(
        geom = "errorbar",
        fun.min = ebbottom,
        fun.max = ebtop,
        width = 0.2
    ) +
    geom_jitter(width = 0.3) +
    geom_signif(
        comparisons = list(
            c("Control", "F5"),
            c("Control", "pAtUbi3:CDS-Rps11-1"),
            c("Control", "pAtUbi3:CDS-Rps11-2")
        ),
        test = t.test,
        test.args = list(
            var.equal = T,
            alternative = "two.side"
        ),
        y_position = c(1.1, 1.3, 1.5),
        annotations = c(""),
        parse = T
    ) +
    annotate(
        geom = "text",
        x = 1.5, y = 1.15,
        label = expression(italic(P) ~ "=" ~ 1.83 %*% 10^-6)
    ) +
    annotate(
        geom = "text",
        x = 2, y = 1.35,
        label = expression(italic(P) ~ "=" ~ 2.71 %*% 10^-5)
    ) +
    annotate(
        geom = "text",
        x = 2.5, y = 1.55,
        label = expression(italic(P) ~ "=" ~ 5.75 %*% 10^-8)
    ) +
    scale_y_continuous(
        expand = c(0, 0),
        limits = c(0, 1.6),
        breaks = seq(0, 1, 0.2)
    ) +
    theme_minimal() +
    theme(
        panel.grid = element_blank(),
        axis.line.y = element_line(),
        axis.ticks.y = element_line(),
        axis.title.y = element_text(
            hjust = 0.25,
            size = 15
        ),
        axis.text.x = element_text(
            angle = 30,
            hjust = 1,
            size = 10
        )
    ) +
    guides(y = guide_axis_truncated(
        trunc_lower = 0,
        trunc_upper = 1
    )) +
    labs(x = NULL, y = "Survival Rate")
p

Prepare data

Define errorbar function

Add errorbar and p-value

Reference