基于R做宏基因组进化树+丰度柱状图TreeBar带聚类树的堆叠柱形图

2023-08-11 阅读量

字数：954字 | 预计阅读时长：5分钟

写在前面

同之前一样，重分析需要所以自己找了各路代码借鉴学习，详情请参考 R语言绘制带聚类树的堆叠柱形图，实操效果如下：

步骤

表格预处理

选取不同样本属水平的物种丰度图（绝对和相对水平都可以，相对画出来是齐的，绝对的bar是不齐的）。Top10丰度外的类群合并为Others。这里注意，用本篇代码时，表格选择csv/txt等格式文件一定要是制表符分隔的，不然会报错重复名或者没有多出的行

分组信息

代码演示

# 装包
install.packages("vegan")

#层次聚类
#读取 OTU 丰度表，csv/txt等文件一定要是制表符分隔的，不然会报错重复名或者没有多出的行
dat <- read.delim('Unigenes.absolute.g.txt', row.names = 1, sep = '\t', head = TRUE, check.names = FALSE)

#计算样本间距离，以群落分析中常用的 Bray-curtis 距离为例
dis_bray <- vegan::vegdist(t(dat), method = 'bray')

#层次聚类，以 UPGMA 为例
tree <- hclust(dis_bray, method = 'average')
tree

plot(tree)

##聚类树绘制
#样本分组颜色、名称等
group <- read.delim('group.txt', row.names = 1, sep = '\t', head = TRUE, check.names = FALSE, stringsAsFactors = FALSE)
grp <- group[2]
group_col <- c('red', 'blue')
names(group_col) <- c('1', '2')
group_name <- c('RA', 'CON')

#样本分组标签
layout(t(c(1, 2, 2, 2, 3)))
par(mar = c(5, 2, 5, 0))

plot(0, type = 'n', xaxt = 'n', yaxt = 'n', frame.plot = FALSE, xlab = '', ylab = '',
     xlim = c(-max(tree$height), 0), ylim = c(0, length(tree$order)))
legend('topleft', legend = group_name, pch = 15, col = group_col, bty = 'n', cex = 1)

#聚类树绘制，按分组给分支上色
treeline <- function(pos1, pos2, height, col1, col2) {
  meanpos = (pos1[1] + pos2[1]) / 2
  segments(y0 = pos1[1] - 0.4, x0 = -pos1[2], y1 = pos1[1] - 0.4, x1 = -height,  col = col1,lwd = 2)
  segments(y0 = pos1[1] - 0.4, x0 = -height,  y1 = meanpos - 0.4, x1 = -height,  col = col1,lwd = 2)
  segments(y0 = meanpos - 0.4, x0 = -height,  y1 = pos2[1] - 0.4, x1 = -height,  col = col2,lwd = 2)
  segments(y0 = pos2[1] - 0.4, x0 = -height,  y1 = pos2[1] - 0.4, x1 = -pos2[2], col = col2,lwd = 2)
}

meanpos = matrix(rep(0, 2 * length(tree$order)), ncol = 2)
meancol = rep(0, length(tree$order))
for (step in 1:nrow(tree$merge)) {
  if(tree$merge[step, 1] < 0){
    pos1 <- c(which(tree$order == -tree$merge[step, 1]), 0)
    col1 <- group_col[as.character(grp[tree$labels[-tree$merge[step, 1]],1])]
  } else {
    pos1 <- meanpos[tree$merge[step, 1], ]
    col1 <- meancol[tree$merge[step, 1]]
  }
  if (tree$merge[step, 2] < 0) {
    pos2 <- c(which(tree$order == -tree$merge[step, 2]), 0)
    col2 <- group_col[as.character(grp[tree$labels[-tree$merge[step, 2]],1])]
  } else {
    pos2 <- meanpos[tree$merge[step, 2], ]
    col2 <- meancol[tree$merge[step, 2]]
  }
  height <- tree$height[step]
  treeline(pos1, pos2, height, col1, col2)
  meanpos[step, ] <- c((pos1[1] + pos2[1]) / 2, height)
  if (col1 == col2) meancol[step] <- col1 else meancol[step] <- 'grey'
}

##堆叠柱形图
#样本顺序调整为和聚类树中的顺序一致
dat <- dat[ ,tree$order]

#物种颜色设置
genus_color <- c('#8DD3C7', '#FFFFB3', '#00CDCD', '#FB8072', '#80B1D3', '#FDB462', '#B3DE69', '#FCCDE5', '#BC80BD', '#CCEBC5', 'gray')
names(genus_color) <- rownames(dat)

#堆叠柱形图
#数字向量，格式为c(bottom, left, top, right)，给出各个方向绘图区边缘空白的大小
par(mar = c(5, 3, 5, 0))

relative <- read.delim('new_Unigenes.relative.g.txt', row.names = 1, sep = '\t', head = TRUE, check.names = FALSE)

bar <- barplot(as.matrix(relative), col = genus_color, space = 0.4, width = 0.7, cex.axis = 1, horiz = TRUE, cex.lab = 1.2,
               xlab = 'Relative Abundance', yaxt = 'n', las = 1, ylim = c(0, ncol(dat)), family = 'mono')

mtext('Top 10 genus', side = 3, line = 1, cex = 1)
text(x = -0.05, y = bar, labels = colnames(dat), col = group_col[group[tree$order, 2]], xpd = TRUE)

#柱形图图例
par(mar = c(5, 1, 5, 0))
plot(0, type = 'n', xaxt = 'n', yaxt = 'n', bty = 'n', xlab = '', ylab = '')
legend('left', pch = 15, col = genus_color, legend = names(genus_color), bty = 'n', cex = 1)

本文作者： twocanis
本文链接： https://twocanis.github.io/2023/08/11/%E5%9F%BA%E4%BA%8ER%E5%81%9A%E5%AE%8F%E5%9F%BA%E5%9B%A0%E7%BB%84%E8%BF%9B%E5%8C%96%E6%A0%91-%E4%B8%B0%E5%BA%A6%E6%9F%B1%E7%8A%B6%E5%9B%BETreeBar/
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