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How to Add P-Values onto Horizontal GGPLOTS
2022-07-02 11:49:00 【Xiaoyu 2022】
library(ggpubr)
library(rstatix)
# Transform `dose` into factor variable
df <- ToothGrowth
df$dose <- as.factor(df$dose)
head(df, 3)
# Box plots
bxp <- ggboxplot(df, x = "dose", y = "len", fill = "dose",
palette = c("#00AFBB", "#E7B800", "#FC4E07"))
# Bar plots showing mean +/- SD
bp <- ggbarplot(df, x = "dose", y = "len", add = "mean_sd", fill = "dose",
palette = c("#00AFBB", "#E7B800", "#FC4E07"))
stat.test <- df %>% t_test(len ~ dose)
# Box plot
stat.test <- stat.test %>% add_xy_position(x = "dose")
bxp + stat_pvalue_manual(stat.test, label = "p.adj.signif", tip.length = 0.01)
# Bar plot
stat.test <- stat.test %>% add_xy_position(fun = "mean_sd", x = "dose")
bp + stat_pvalue_manual(stat.test, label = "p.adj.signif", tip.length = 0.01)
library(ggpubr)
library(rstatix)
# Transform `dose` into factor variable
df <- ToothGrowth
df$dose <- as.factor(df$dose)
head(df, 3)
# Box plots
bxp <- ggboxplot(df, x = "dose", y = "len", fill = "dose",
palette = c("#00AFBB", "#E7B800", "#FC4E07"))
# Bar plots showing mean +/- SD
bp <- ggbarplot(df, x = "dose", y = "len", add = "mean_sd", fill = "dose",
palette = c("#00AFBB", "#E7B800", "#FC4E07"))
stat.test <- stat.test %>% add_xy_position(x = "dose")
bxp +
stat_pvalue_manual(
stat.test, label = "p.adj.signif", tip.length = 0.01,
coord.flip = TRUE
) +
coord_flip()
# Horizontal bar plot with p-values
stat.test <- stat.test %>% add_xy_position(fun = "mean_sd", x = "dose")
bp + stat_pvalue_manual(
stat.test, label = "p.adj.signif", tip.length = 0.01,
coord.flip = TRUE
) +
coord_flip()
library(ggpubr)
library(rstatix)
# Transform `dose` into factor variable
df <- ToothGrowth
df$dose <- as.factor(df$dose)
head(df, 3)
# Box plots
bxp <- ggboxplot(df, x = "dose", y = "len", fill = "dose",
palette = c("#00AFBB", "#E7B800", "#FC4E07"))
# Bar plots showing mean +/- SD
bp <- ggbarplot(df, x = "dose", y = "len", add = "mean_sd", fill = "dose",
palette = c("#00AFBB", "#E7B800", "#FC4E07"))
# Using `p.adj` as labels
stat.test <- stat.test %>% add_xy_position(x = "dose")
bxp +
stat_pvalue_manual(
stat.test, label = "p.adj", tip.length = 0.01,
coord.flip = TRUE
) +
coord_flip()
library(ggpubr)
library(rstatix)
# Transform `dose` into factor variable
df <- ToothGrowth
df$dose <- as.factor(df$dose)
head(df, 3)
# Box plots
bxp <- ggboxplot(df, x = "dose", y = "len", fill = "dose",
palette = c("#00AFBB", "#E7B800", "#FC4E07"))
# Bar plots showing mean +/- SD
bp <- ggbarplot(df, x = "dose", y = "len", add = "mean_sd", fill = "dose",
palette = c("#00AFBB", "#E7B800", "#FC4E07"))
stat.test <- df %>% t_test(len ~ dose, ref.group = "0.5")
# Vertical box plot with p-values
stat.test <- stat.test %>% add_xy_position(x = "dose")
bxp +
stat_pvalue_manual(stat.test, label = "p.adj", tip.length = 0.01) +
scale_y_continuous(expand = expansion(mult = c(0.05, 0.1)))
library(ggpubr)
library(rstatix)
# Transform `dose` into factor variable
df <- ToothGrowth
df$dose <- as.factor(df$dose)
head(df, 3)
# Box plots
bxp <- ggboxplot(df, x = "dose", y = "len", fill = "dose",
palette = c("#00AFBB", "#E7B800", "#FC4E07"))
# Bar plots showing mean +/- SD
bp <- ggbarplot(df, x = "dose", y = "len", add = "mean_sd", fill = "dose",
palette = c("#00AFBB", "#E7B800", "#FC4E07"))
stat.test <- df %>% t_test(len ~ dose, ref.group = "0.5")
# Vertical box plot with p-values
# Vertical bar plot with p-values
stat.test <- stat.test %>% add_xy_position(fun = "mean_sd", x = "dose")
bp +
stat_pvalue_manual(stat.test, label = "p.adj.signif", tip.length = 0.01) +
scale_y_continuous(expand = expansion(mult = c(0.05, 0.1)))
library(ggpubr)
library(rstatix)
# Transform `dose` into factor variable
df <- ToothGrowth
df$dose <- as.factor(df$dose)
head(df, 3)
# Box plots
bxp <- ggboxplot(df, x = "dose", y = "len", fill = "dose",
palette = c("#00AFBB", "#E7B800", "#FC4E07"))
# Bar plots showing mean +/- SD
bp <- ggbarplot(df, x = "dose", y = "len", add = "mean_sd", fill = "dose",
palette = c("#00AFBB", "#E7B800", "#FC4E07"))
# Horizontal box plot with p-values
stat.test <- stat.test %>% add_xy_position(x = "dose")
bxp +
stat_pvalue_manual(
stat.test, label = "p.adj", tip.length = 0.01,
coord.flip = TRUE
) +
scale_y_continuous(expand = expansion(mult = c(0.05, 0.1))) +
coord_flip()
library(ggpubr)
library(rstatix)
# Transform `dose` into factor variable
df <- ToothGrowth
df$dose <- as.factor(df$dose)
head(df, 3)
# Box plots
bxp <- ggboxplot(df, x = "dose", y = "len", fill = "dose",
palette = c("#00AFBB", "#E7B800", "#FC4E07"))
# Bar plots showing mean +/- SD
bp <- ggbarplot(df, x = "dose", y = "len", add = "mean_sd", fill = "dose",
palette = c("#00AFBB", "#E7B800", "#FC4E07"))
# Horizontal bar plot with p-values
stat.test <- stat.test %>% add_xy_position(fun = "mean_sd", x = "dose")
bp +
stat_pvalue_manual(
stat.test, label = "p.adj", tip.length = 0.01,
coord.flip = TRUE
) +
scale_y_continuous(expand = expansion(mult = c(0.05, 0.1))) +
coord_flip()
library(ggpubr)
library(rstatix)
# Transform `dose` into factor variable
df <- ToothGrowth
df$dose <- as.factor(df$dose)
head(df, 3)
# Box plots
bxp <- ggboxplot(df, x = "dose", y = "len", fill = "dose",
palette = c("#00AFBB", "#E7B800", "#FC4E07"))
# Bar plots showing mean +/- SD
bp <- ggbarplot(df, x = "dose", y = "len", add = "mean_sd", fill = "dose",
palette = c("#00AFBB", "#E7B800", "#FC4E07"))
# Show p-values at x = "group2"
stat.test <- stat.test %>% add_xy_position(x = "dose")
bxp +
stat_pvalue_manual(
stat.test, label = "p = {p.adj}", tip.length = 0.01,
coord.flip = TRUE, x = "group2", hjust = 0.4
) +
scale_y_continuous(expand = expansion(mult = c(0.05, 0.2))) +
coord_flip()
library(ggpubr)
library(rstatix)
# Transform `dose` into factor variable
df <- ToothGrowth
df$dose <- as.factor(df$dose)
head(df, 3)
# Box plots
bxp <- ggboxplot(df, x = "dose", y = "len", fill = "dose",
palette = c("#00AFBB", "#E7B800", "#FC4E07"))
# Bar plots showing mean +/- SD
bp <- ggbarplot(df, x = "dose", y = "len", add = "mean_sd", fill = "dose",
palette = c("#00AFBB", "#E7B800", "#FC4E07"))
# Make the p-values horizontal using the option angle
stat.test <- stat.test %>% add_xy_position(x = "dose")
bxp +
stat_pvalue_manual(
stat.test, label = "p = {p.adj}", tip.length = 0.01,
coord.flip = TRUE, x = "group2", angle = 90
) +
scale_y_continuous(expand = expansion(mult = c(0.05, 0.1))) +
scale_x_discrete(expand = expansion(mult = c(0.05, 0.3))) +
coord_flip()
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