ggplot2绘图实例第一回——生物信息学物种丰度的堆叠图

原图片链接：https://media.springernature.com/full/springer-static/image/art%3A10.1038%2Fs41467-019-11682-z/MediaObjects/41467_2019_11682_Fig1_HTML.png?as=webp

R语言绘制结果

                                        

数据链接：

data_1:https://static-content.springer.com/esm/art%3A10.1038%2Fs41467-019-11682-z/MediaObjects/41467_2019_11682_MOESM4_ESM.xlsx

data_5:https://static-content.springer.com/esm/art%3A10.1038%2Fs41467-019-11682-z/MediaObjects/41467_2019_11682_MOESM8_ESM.xlsx

1. 数据读取和数据整合：

library(tidyverse)
library(readxl)
data <- read_xlsx("data_1.xlsx",col_names = TRUE,range = "B3:Z1151")
data_extracted<-extract(data,`Taxonomic classification`, into=c('Domain', 'Phylum', 'Genus'),'k__([A-z]*);p__(.*);c__.*g__(.*);', convert=TRUE)
data_extracted[which(data_extracted$Phylum == "",arr.ind = TRUE),]$Phylum="Unknown"
data_extracted[which(data_extracted$Genus == "",arr.ind = TRUE),]$Genus="Unknown"
data_sum<-data_extracted %>% gather(wipe,abundant,-Domain,-Phylum,-Genus)

data的数据结构：

>str(data)     ##该命令可用于查看数据结构

Classes ‘tbl_df’, ‘tbl’ and 'data.frame':    1148 obs. of  25 variables:
 $ Taxonomic classificat