顶刊图社 | 第001期：分面堆积柱状图
附上代码：
###Stacked bar plot####Reference:#Muñoz, K.A., Ulrich, R.J., Vasan, A.K. et al. A Gram-negative-selective antibiotic that spares the gut microbiome. Nature 630, 429–436 (2024).#https://doi.org/10.1038/s41586-024-07502-0#Original figure：https://www.nature.com/articles/s41586-024-07502-0/figures/5#install.packages("pacman") #如果没有pacman，请先安装，pacman是一个管理R包的工具library(pacman)p_load(reshape2)getwd()#由于作者没有提供原始数据，这里生成10行，24列的随机数据用于画图set.seed(123) #设置随机种子，方便复现d1 <- matrix(runif(6 * 24, min = 0, max = 0.05), nrow = 6, ncol = 24) #生成均匀分布的随机数d2 <- matrix(runif(4 * 24, min = 0.3, max = 0.6), nrow = 4, ncol = 24)#生成均匀分布的随机数df <- rbind(d1,d2)#按行合并两个数据框df <- apply(df, 2, function(x) x / sum(x)) #按列归一化df <- as.data.frame(df)microbes <- paste0("Microbe_", 1:10)df$microbes <- microbesdf <- melt(df,id.vars = "microbes") #宽数据转为长数据df$sample<- rep(1:24, each = 10)df$day <- c(rep("Day 0",60),rep("Day 7",60), rep("Day 10",60), rep("Day 31",60))df$day <- factor(df$day,levels = c("Day 0","Day 7","Day 10","Day 31"))df$microbes <- factor(df$microbes,levels = c("Microbe_7","Microbe_4","Microbe_2","Microbe_9","Microbe_5","Microbe_8","Microbe_1","Microbe_3","Microbe_6","Microbe_10"))p <- ggplot(data = df,aes(x = sample,y = value, fill = microbes)) +geom_bar(stat = "identity",position = "stack") + #绘制堆积柱状图，使用原始数值，并进行堆积labs(title = "",subtitle = "Vehicle") + #设置标题和副标题labs(x = "", y = "Relative abundance",fill = "Family") +#设置坐标轴标签和图例标题#手动设置配色方案scale_fill_manual(values = c( "Microbe_1"="#D3D1D2", "Microbe_2"="#CC79A8", "Microbe_3"="#7AC0EA", "Microbe_4"="#0EA079","Microbe_5"="#68C49D","Microbe_6"="#EACEDF", "Microbe_7"="#5AB4E5","Microbe_8"="#D99BBB","Microbe_9"="#98D1F0", "Microbe_10"="#7F7F7F")) +scale_y_continuous(limits = c(0, 1), expand = c(0.02, 0))+ #limits设置刻度范围；expand = c(lower, upper)：用于设置坐标轴的扩展范围。theme_classic()+theme(plot.subtitle = element_text(color = "black", size = 14),axis.text = element_text(color = "black", size = 14),axis.title = element_text(color = "black", size = 14),axis.text.x = element_blank(), #隐藏X轴文本axis.ticks.x = element_blank(),#隐藏X轴刻度strip.text.x = element_text(size = 14),strip.background = element_blank(),strip.placement = "outside", #facet标签将显示在绘图区域外部legend.position = "right",legend.title = element_text(size = 12),legend.text = element_text(size = 11),legend.key.size = unit(0.4, "cm"),legend.key.spacing.y = unit(0.2, "cm"),panel.spacing = unit(0.05, "lines"),panel.grid.major = element_blank(),panel.grid.minor = element_blank(),panel.background = element_blank())+facet_grid(~ day,scales = "free", switch="both")#分面标签通常展示在plot的上面或右面，switch参数设置为x，上面的标签会放到下面；switch参数设置为y，右面的标签会放到左边，设置为both，相当于x+y#https://stackoverflow.com/questions/3261597/change-the-position-of-the-strip-label-in-ggplot-from-the-top-to-the-bottompggsave(filename = "Stacked bar plot.pdf", plot =p, height = 4, width = 6 )
Muñoz, K.A., Ulrich, R.J., Vasan, A.K. et al. A Gram-negative-selective antibiotic that spares the gut microbiome. Nature 630, 429–436 (2024). https://doi.org/10.1038/s41586-024-07502-0
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