ggplot2做图（填坑中）

数据

df <- data.frame(x = 1:10, y = 1:10, row.names = paste0("s", 1:10))
metadata <- data.frame(f1 = c(rep("A", 5), rep("B", 5)), 
                 f2 = c(rep("C", 3), rep("D", 4), rep("E", 3)),
                 row.names = paste0("s", 1:10))

结果存储

outdir <- "plots"
if(! dir.exists(outdir)) { # 判断目录是否存在
  dir.create(outdir) # 创建目录
}

做图

1. 散点图 (scatter plot)

library(ggplot2)
library(ggpubr)

# scatter plot
Scatter_plot <- function(df, metadata) {
  identical(rownames(df), rownames(metadata)) # 判断df和metadata的行名是否完全一致（内容和顺序）
  data <- cbind(df, metadata) # 按列合并df和metadata
  ggplot(data, aes(x = x, y = y, color = f1)) + 
    geom_point() +
    geom_smooth(method = lm, linetype = 1, se = FALSE, span = 1) + # 趋势线
    stat_cor(method = "spearman",label.x = 4, label.y = 9) + # library(ggpubr)
    expand_limits(x = c(0, 12), y = c(0, 12)) + # 设置坐标轴范围
    xlab("X") + # 设置X轴名称
    ylab("Y") + # 设置Y轴名称
    scale_color_discrete(name = "Group") + # 设置图例名称
    theme_bw() + 
    theme(panel.grid.major = element_blank(),
          panel.grid.minor = element_blank(),
          panel.background = element_blank(),
          axis.text.x = element_text(angle = 90, hjust = 0.5, vjust = 0.5))
}

scatter_plot <- Scatter_plot(df, metadata)
ggsave(filename = paste0(outdir, "/scatter_plot.pdf"), plot = scatter_plot, width = 5, height = 5)

2. 箱型图 (box plot)

# box plot
Boxplot <- function(df, metadata) {
  identical(rownames(df), rownames(metadata)) # 判断df和metadata的行名是否完全一致（内容和顺序）
  data <- cbind(df, metadata) # 按列合并df和metadata
  ggplot(data, aes(x = f1, y = y, color = f1)) +
    geom_boxplot(outlier.shape = NA) +
    scale_colour_manual(values = brewer.pal(8, "Pastel2")) +
    geom_jitter(aes(color = f1), shape = 1, width = 0.2) +
    facet_wrap(~f1 + f2, scales = "free_x") +
    xlab("X") + 
    ylab("Y") + 
    theme_bw() + 
    theme(panel.grid.major = element_blank(),
          panel.grid.minor = element_blank(),
          panel.background = element_blank())
}

boxplot <- Boxplot(df, metadata)
ggsave(filename = paste0(outdir, "/box_plot.pdf"), plot = scatter_plot, width = 5, height = 5)

# box plot with wilcoxon test
Boxplot2 <- function(df, metadata) {
  identical(rownames(df), rownames(metadata)) # 判断df和metadata的行名是否完全一致（内容和顺序）
  data <- cbind(df, metadata) # 按列合并df和metadata
  ggplot(data, aes(x = f2, y = y, color = f2)) +
    geom_boxplot(outlier.shape = NA) +
    scale_colour_manual(values = brewer.pal(8, "Pastel2")) +
    geom_jitter(aes(color = f2), shape = 1, width = 0.2) +
    geom_signif(comparisons = list(c("C", "D"), c("C", "E")), 
                test = "wilcox.test", textsize = 2, step_increase = 0.1,
                test.args = list(exact = FALSE, correct = FALSE, conf.int = TRUE, 
                conf.level = 0.95)) + # 添加wilcoxon test结果，并使不同分组的检验间隔0.01
    xlab("X") + 
    ylab("Y") + 
    theme_bw() + 
    theme(panel.grid.major = element_blank(),
          panel.grid.minor = element_blank(),
          panel.background = element_blank())
}

boxplot2 <- Boxplot2(df, metadata)
ggsave(filename = paste0(outdir, "/box_plot2.pdf"), plot = boxplot, width=5, height=5)

3. 柱状图 (bar plot)

4. 堆积柱状图 (stacked bar chart)

5. 热图 (heatmap)

6. 三元相图 (Ternary plot)

代码