R绘图 | 一幅小提琴图的美化之旅

# 加载包
library(tidyverse)
library(ggplot2)
# 示例数据准备
niwot_plant_exp <- read.csv("niwot_plant_exp.csv")
# Calculate species richness per plot per year
niwot_richness <- niwot_plant_exp %>% 
  group_by(plot_num, year) %>%
  mutate(richness = length(unique(USDA_Scientific_Name))) %>% 
  ungroup()
distributions1 <- ggplot(niwot_richness, aes(x = fert, y = richness)) +
    geom_violin()
distributions1

theme_niwot <- function(){
  theme_bw() +
    theme(text = element_text(family = "Helvetica Light"),
          axis.text = element_text(size = 16), 
          axis.title = element_text(size = 18),
          axis.line.x = element_line(color="black"), 
          axis.line.y = element_line(color="black"),
          panel.border = element_blank(),
          panel.grid.major.x = element_blank(),                                          
          panel.grid.minor.x = element_blank(),
          panel.grid.minor.y = element_blank(),
          panel.grid.major.y = element_blank(),  
          plot.margin = unit(c(1, 1, 1, 1), units = , "cm"),
          plot.title = element_text(size = 18, vjust = 1, hjust = 0),
          legend.text = element_text(size = 12),          
          legend.title = element_blank(),                              
          legend.position = c(0.95, 0.15), 
          legend.key = element_blank(),
          legend.background = element_rect(color = "black", 
                                           fill = "transparent", 
                                           size = 2, linetype = "blank"))
}
distributions2 <- ggplot(niwot_richness, aes(x = fert, y = richness)) +
  geom_violin(aes(fill = fert, colour = fert), alpha = 0.5) +
  # alpha控制不透明度
  theme_niwot()

distributions3 <- ggplot(niwot_richness, aes(x = fert, y = richness)) +
  geom_violin(aes(fill = fert, colour = fert), alpha = 0.5) +
  geom_boxplot(aes(colour = fert), width = 0.2) + # 添加箱线图图层
  theme_niwot()

distributions4 <- ggplot(niwot_richness, aes(x = fert, y = richness)) +
  geom_violin(aes(fill = fert, colour = fert), alpha = 0.5) +
  geom_jitter(aes(colour = fert), position = position_jitter(0.1), # 添加散点
              alpha = 0.3) +
  theme_niwot()

# This code loads the function in the working environment
source("geom_flat_violin.R") 
distributions5 <- 
  ggplot(data = niwot_richness, 
         aes(x = reorder(fert, desc(richness)), y = richness, fill = fert)) +
  # 半小提琴
  geom_flat_violin(position = position_nudge(x = 0.2, y = 0), alpha = 0.8) +
  # 散点
  geom_point(aes(y = richness, color = fert), 
             position = position_jitter(width = 0.15), size = 1, alpha = 0.1) +
  # 箱线
  geom_boxplot(width = 0.2, outlier.shape = NA, alpha = 0.8) +
  # \n 添加一个新行，在轴和轴标题之间创建一些空间
  labs(y = "Species richness\n", x = NULL) +
  # 删除图例
  guides(fill = FALSE, color = FALSE) +
  # 设置 y 轴范围
  scale_y_continuous(limits = c(0, 30)) +
  # 颜色
  scale_fill_manual(values = c("#5A4A6F", "#E47250",  "#EBB261", "#9D5A6C")) +
  scale_colour_manual(values = c("#5A4A6F", "#E47250",  "#EBB261", "#9D5A6C")) +
  theme_niwot()
distributions5

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