R语言绘图 | 双Y轴截断图

news2024/11/22 23:19:53

教程原文：双Y轴截断图绘制教程

本期教程

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往期教程部分内容

教程来源：
Yunyun Gao, Hao Luo, Yong-Xin Liu,et al, Benchmarking metagenomics tools for purging host contamination.

绘图代码

library(ggplot2)
library(tidyverse)
library(ggbreak)
library(dunn.test)
library(car)

data <- read.table("data.txt", head = TRUE, sep = "\t")

# Select the relevant columns for data1
data1 <- data[, c("Software", "Taxa", "Rss")]
data2 <- data[, c("Software", "Taxa", "Time")]

data1$Software <- factor(data1$Software, levels = c( "BWA","Bowtie2","Kneaddata", "KMCP", "Kraken2", "Krakenuniq"))

ggplot(data1) +
  geom_col(aes(x = Software, y = Rss, fill = Taxa), position = 'dodge', width = 0.8) +
  scale_fill_manual(values = c('Rice' = '#fec79e', 'Human' = '#8ec4cb')) +
  labs(x = "Software", y = "Memory usage / Gigabytes") +
  theme_minimal() +
  theme_test(base_size = 24) +
  theme(
    legend.position = 'none',
    panel.border = element_rect(size = 2, fill = 'transparent'),
    axis.text = element_text(color = 'black'),
    axis.text.x = element_text(angle = 45, hjust = 1)  # Rotate x-axis labels for better visibility
  ) +
  geom_rect(aes(xmin = 0.5, xmax = 0.8, ymin = 53, ymax = 57), fill = '#8ec4cb', color = '#8ec4cb') +
  geom_rect(aes(xmin = 1.4, xmax = 1.7, ymin = 53, ymax = 57), fill = '#fec79e', color = '#fec79e') +
  annotate(geom = 'text', x = 1.9, y = 55, label = 'Rice', size = 7) +
  annotate(geom = 'text', x = 1.1, y = 55, label = 'Human', size = 7) +
  scale_y_continuous(
    breaks = c(seq(0, 10, 10), seq(5, 10, 5), seq(20, 60, 10)),
    limits = c(0, 60),
    expand = c(0, 0),
    sec.axis = sec_axis(~ .*5, name = 'Time consumption / minutes', breaks = c(seq(0, 50, 25), seq(50, 300, 50)))
  ) +
  geom_point(data = data2, aes(x = factor(Software), y = Time * 0.2, color = Taxa, group = Taxa), shape=17, size = 5, na.rm = TRUE) +
  scale_color_manual(values = c('#1e8b9b', '#ff8c3e')) +
  scale_y_break(c(6,11), space = 0, scales = 1.8)

Check Time of all taxa, Normality test

shapiro_test <- by(data$Time, data$Taxa, shapiro.test)

# Extract p-values from each group's test results
p_values <- sapply(shapiro_test, function(x) x$p.value)

# Check if each group conforms to normal distribution
normal_data <- p_values > 0.05

if (all(normal_data)) {
summary_stats <- aggregate(Time ~ Taxa, data = data, FUN = function(x) c(mean = mean(x), se = sd(x)/sqrt(length(x))))
print(summary_stats)
} else {
summary_stats <- aggregate(Time ~ Taxa, data = data, FUN = function(x) c(median = median(x), p25 = quantile(x, 0.25), p75 = quantile(x, 0.75)))
print(summary_stats)
}
#>    Taxa Time.mean   Time.se
#> 1 Human 99.474900 35.348141
#> 2  Rice  8.478217  2.883665

levene_test_result <- leveneTest(Time ~ Taxa, data = data)
p_value_levene <- levene_test_result$`Pr(>F)`[1]

if (all(normal_data)) {
if (p_value_levene > 0.05) {
  t_test_result <- t.test(Time ~ Taxa, data = data, paired = TRUE)
  print(t_test_result)
} else {
  wilcox_result <- wilcox.test(Time ~ Taxa, data = data, paired = TRUE)
  print(wilcox_result)
}
} else {
wilcox_result <- wilcox.test(Time ~ Taxa, data = data, paired = TRUE)
print(wilcox_result)
}
#> 
#>  Wilcoxon signed rank exact test
#> 
#> data:  Time by Taxa
#> V = 21, p-value = 0.03125
#> alternative hypothesis: true location shift is not equal to 0

shapiro_test <- by(data$Rss, data$Taxa, shapiro.test)

# Extract p-values from each group's test results
p_values <- sapply(shapiro_test, function(x) x$p.value)

# Check if each group conforms to normal distribution
normal_data <- p_values > 0.05

if (all(normal_data)) {
  summary_stats <- aggregate(Rss ~ Taxa, data = data, FUN = function(x) c(mean = mean(x), se = sd(x)/sqrt(length(x))))
  print(summary_stats)
} else {
  summary_stats <- aggregate(Rss ~ Taxa, data = data, FUN = function(x) c(median = median(x), p25 = quantile(x, 0.25), p75 = quantile(x, 0.75)))
  print(summary_stats)
}
#>    Taxa Rss.median Rss.p25.25% Rss.p75.75%
#> 1 Human  5.6300000   4.8150000  18.2650000
#> 2  Rice  0.8040332   0.5614160   2.1725659

levene_test_result <- leveneTest(Rss ~ Taxa, data = data)
p_value_levene <- levene_test_result$`Pr(>F)`[1]

if (all(normal_data)) {
  if (p_value_levene > 0.05) {
    t_test_result <- t.test(Rss ~ Taxa, data = data, paired = TRUE)
    print(t_test_result)
  } else {
    wilcox_result <- wilcox.test(Rss ~ Taxa, data = data, paired = TRUE)
    print(wilcox_result)
  }
} else {
  wilcox_result <- wilcox.test(Rss ~ Taxa, data = data, paired = TRUE)
  print(wilcox_result)
}
#> 
#>  Wilcoxon signed rank exact test
#> 
#> data:  Rss by Taxa
#> V = 21, p-value = 0.03125
#> alternative hypothesis: true location shift is not equal to 0