主要物种丰度冲击条形图

最新推荐文章于 2024-01-05 16:34:25 发布

wilzjdba

最新推荐文章于 2024-01-05 16:34:25 发布

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本文链接：https://blog.csdn.net/wlzjdba/article/details/107363239

版权

本文介绍如何使用QIIME软件处理得到的txt格式相对物种丰度数据，探讨如何通过条形图展示不同物种的丰度情况。

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数据来源

QIIME中得到的txt格式相对物种丰度数据表

Palette <-c("#B2182B","#E69F00","#56B4E9","#009E73","#F0E442","#0072B2","#D55E00","#CC79A7","#CC6666","#9999CC","#66CC99","#999999","#ADD1E5")

abundance <- read.table("otu_taxa_table_L2.txt",header = TRUE,sep = "\t")
abundance <- as.data.frame(abundance)
taxon <- gsub(".*(p__)","",abundance$Taxon)
taxon <- gsub(".*(Bacteria;)","",taxon)
taxon <- gsub(".*(Other)","",taxon)
taxon <- gsub("(\\[)","",taxon)
taxon <- gsub("(\\])","",taxon)
abundance$Taxon <- taxon
abundance[abundance==""] <- NA
abundance <- na.omit(abundance)
abundance <- t(abundance)
colnames(abundance) <- abundance[1,]
abundance <- abundance[-1,]
abundance <- a