微生物多样性qiime2分析流程(10) 数据可视化分析(中) 之绘制物种组成图

前面一系列可视化教程，都是通过将数据整合成phyloseq对象再运用MicrobiotaProcess包已经封装好的函数进行可视化操作，虽然简洁好用，但是灵活性不足，现在让我们根据已有数据来一套组合拳

1.Hcluster_bar

phylum.xls，otu_table.xls文件可根据之前介绍步骤导出

1.1 自定义颜色

rm(list = ls())
pacman::p_load(tidyverse,reshape,ggtree,aplot,RColorBrewer)   
colors <-c("#E41A1C","#1E90FF","#FF8C00","#4DAF4A","#984EA3",
           "#40E0D0","#FFC0CB","#00BFFF","#FFDEAD","#90EE90",
           "#EE82EE","#00FFFF","#F0A3FF", "#0075DC","#993F00",
           "#4C005C","#2BCE48","#FFCC99","#808080","#94FFB5",
           "#8F7C00","#9DCC00","#C20088","#003380","#FFA405",
           "#FFA8BB","#426600","#FF0010","#5EF1F2","#00998F",
           "#740AFF","#990000","#FFFF00")

1.2 读入数据绘制行聚类树

p <- read.delim("otu_table.xls",header = T,
                sep="\t",check.names = F,row.names = 1) %>% t()

tree <- hclust(dist(p)) %>% 
  ggtree(layout="rectangular", branch.length="none")

1.3 绘制水平柱状图

bar <- read.delim("phylum.xls",header = T,
                  sep="\t",check.names = F) %>% 
  melt() %>% ggplot(aes(variable ,value,fill=OTU))+
  geom_bar(stat="identity")+labs(x="",y="")+
  theme_bw()+
  theme(axis.title.x=element_blank(),
        axis.text.x=element_blank(),
        axis.ticks.x=element_blank())+
  scale_fill_manual(values = colors)+labs(fill="taxon")+
  scale_y_continuous(expand=c(0,0))+coord_flip()

1.4 aplot包将聚类树与柱状图拼接

bar%>%insert_left(tree,width=.3)

treebar_phylum.jpeg

适合大数据的聚类圈图

rm(list = ls())
pacman::p_load(tidyverse,reshape,ggtree,ggtreeExtra,ggnewscale)   
col <- c(34, 51, 142, 26, 31, 371, 
           36, 7, 12, 30, 84, 88, 116, 
           121, 77, 56, 386, 373, 423, 
           435, 438, 471, 512, 130, 52, 
           47, 6, 11, 43, 54, 367, 382, 
           422, 4, 8, 375, 124, 448, 419, 
           614, 401, 403, 613, 583, 652, 
           628, 633, 496, 638, 655, 132, 503, 24)
mycolors <- c(col,colors()[rep(col,5)])
p <- read.tree("otu_hc.tre") %>%
  ggtree(branch.length = "none", layout = "fan", size = 0.3)
dat <- read.delim("phylum.xls") %>% melt()
p2 <- p +
  new_scale_fill() +
  geom_fruit(data = dat,
             mapping = aes(x = value, fill = OTU.ID, y = variable),
             geom = geom_bar,orientation = "y",stat = "identity") +
  geom_tiplab(offset = 7, size = 1)+
  scale_fill_manual(values = mycolors)
p2

Hcluster_bar.jpg

2. 物种组成柱状图

绘制之前需要先对属水平数据进行过滤，可根据https://www.jianshu.com/p/e1dde3571d16中的代码对数据进行过滤

2.1 数据过滤

rm(list=ls())
colors <-c("#E41A1C","#1E90FF","#FF8C00","#4DAF4A","#984EA3",
           "#40E0D0","#FFC0CB","#00BFFF","#FFDEAD","#90EE90",
           "#EE82EE","#00FFFF","#F0A3FF", "#0075DC", 
           "#993F00","#4C005C","#2BCE48","#FFCC99",
           "#808080","#94FFB5","#8F7C00","#9DCC00",
           "#C20088","#003380","#FFA405","#FFA8BB",
           "#426600","#FF0010","#5EF1F2","#00998F",
           "#740AFF","#990000","#FFFF00")

pacman::p_load(tidyverse,magrittr,reshape,RColorBrewer,ggtree)
computed_persent <- function(path) {
  data <- path %>%
    read.delim(check.names = FALSE, row.names = 1)
  data2 <- data %>%
    mutate(sum = rowSums(.), persent = sum / sum(sum) * 100, sum = NULL,) %>%
    rbind(filter(., persent < 1) %>% colSums()) %>%
    mutate(OTU= c(data %>% rownames(),"others"))
  filter(data2[1:(nrow(data2) - 1),], persent > 1) %>%
    rbind(data2[nrow(data2),]) %>%
    select(ncol(.), 1:(ncol(.) - 2)) %>%
    set_rownames(seq_len(nrow(.))) %>%
    return()
}
path <- "genus.xls"

2.2 整合分组文件

a1 <- computed_persent(path) %>% melt()
a2 <- "group.txt" %>% read.delim()
a4 <- NULL

for (i in seq_len(nrow(a1))) { 
  a4[i] <- a2[which(a2[, 1] == a1[i, 2]), 2] }

a1[, 4] <- a4
a1

2.3 ggplot2可视化

ggplot(a1,aes(variable,value,fill=OTU))+
  geom_bar(stat="identity",position = "fill")+
  facet_grid(. ~ V4,scales = "free",space="free_x")+
  labs(x="",y="Proportions")+
  scale_fill_manual(values = colors)+labs(fill="")+
  theme(legend.title=element_blank())+
  scale_y_continuous(expand=c(0,0))+theme_bw()

bar.jpeg

感谢身边的大佬朋友提供代码，没有他的支援某些步骤没法这么顺利进行

未完待续......

最后编辑于：2021.01.11 16:49:20