条形堆积图

照例，先放结果图

代码如下：

1.导入数据

# 导入数据并查看数据集格式

rm(list = ls())##清除之前命令

setwd("D:\\R_base\\Rstudio_workfile\\Co_occurrence\\3_genderage")

phylum <- read.delim('profile_phylumtop20.txt', sep="\t", header=T, row.names=1)

head(phylum)

2.数据处理

# 将绝对丰度转化为百分比形式的相对丰度

phylum_per <- as.data.frame(lapply(phylum, function(x) x / sum(x)))

row.names(phylum_per) <- row.names(phylum) #加一下行名

# 计算每个门水平的平均丰度便于后续筛选

phylum.ave <- apply(phylum_per, 1, FUN=mean)

phylum.2 <- cbind(phylum_per, phylum.ave)[order(-phylum.ave),] #排个序

# 选择丰度最高的10个门剩下的放入others里

phylum.2 <- subset(phylum.2[1:10,], select=-phylum.ave)

# 统计others丰度

phylum.2 <- rbind(phylum.2, others=apply(phylum.2, 2, function(x){1-sum(x)}))

# 加一列行名便于后续的长宽转换

phylum.2 <- cbind(PhylumID=row.names(phylum.2), phylum.2)

# 长宽转换

library(reshape2)

# 因子排个序

phylum.2$PhylumID <- factor(phylum.2$PhylumID, levels = rev(phylum.2$PhylumID))

phylum.gg <- melt(phylum.2, id.vars="PhylumID", variable.name="SampleID", value.name="Abundance")

head(phylum.gg)

# 添加分组信息

phylum.gg$group <- c(rep('S', 132), rep('M', 154), rep('L', 132)) # 根据样本情况设置

3.绘图

# 为了复现文章中的图需要的颜色包

library(wesanderson) ##install.packages("wesanderson")

library(colortools) ##remotes::install_github("gastonstat/colortools")

library(ggpubr)

ggbarplot(phylum.gg, x = "SampleID", y="Abundance", color="black", fill="PhylumID", legend="right", legend.title="Top Phylum", main="Relative counts per Phylum", font.main = c(14,"bold", "black"), font.x = c(12, "bold"), font.y=c(12,"bold")) +

theme_bw() +

rotate_x_text() +

scale_fill_manual(values=c("gray",rev(wheel("skyblue3")[1:10]))) + # 颜色设置

facet_grid(~ group, scales = "free_x", space='free') +

labs(x = "Sample", y = "Relative proportion") +

theme(axis.text.x=element_blank(), axis.ticks.x=element_blank(),

axis.title = element_text(face = "bold"),

plot.title = element_text(face = "bold"),

legend.title = element_text(face = "bold"))

ggsave(filename = "relative_counts.pdf", device="pdf", width=8, height=4)

##数据示例（OTU绝对丰度表）