Guorui Zhong - Add errorbar and p-value on barplot with ggsignif

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