將feature_table_with_taxonomy.xlsx另存為txt文件，然后將txt文件第一列列名“feature ID”改為“#OTU ID”，最后一列列名“Taxonomy”改為“Consensus Lineage”。
將代表序列文件2_feature_rep_seq.fasta和5_metadata_se.txt放到同目錄下。
library("phyloseq")
library("ggplot2")
library(MicrobiotaProcess)
windowsFonts(TNM = windowsFont('Times New Roman'))#設(shè)置字體
qiimedata <- import_qiime(otufilename = "feature_table_with_taxonomy.txt",
mapfilename = "5_metadata_se.txt",
#treefilename = "tree.rooted.nwk",
refseqfilename = "2_feature_rep_seq.fasta"
)
Processing map file...
Processing otu/tax file...
Reading file into memory prior to parsing...
Detecting first header line...
Header is on line 1
Converting input file to a table...
Defining OTU table...
Parsing taxonomy table...
Processing Reference Sequences...
qiimedata@sam_data[["group"]]<-factor(qiimedata@sam_data[["group"]],levels = c("CON","HFD","HFD+FA"))
colnames(qiimedata@tax_table@.Data)[1]<-"Kingdom"
phytax <- get_taxadf(qiimedata, taxlevel=2)
phybar <- ggbartax(obj=phytax,facetNames="group", count=FALSE,plotgroup=TRUE) +
xlab(NULL) + ylab("Relative abundance (%)")+
theme_pubr()+
theme(axis.text.x = element_text(face="bold",family = "TNM",size=2),
axis.text.y = element_text(face="bold",family = "TNM",size=15),
axis.title.y = element_text(face="bold",family = "TNM",size=25))+
theme(legend.position="right",legend.title=element_text(family="TNM",face="bold", size=20))+
theme(legend.text = element_text(size = 13, face="bold",family="TNM"))
phybar
phytax <- get_taxadf(qiimedata, taxlevel=6)
phybar <- ggbartax(obj=phytax,facetNames="group", count=FALSE,plotgroup=TRUE) +
xlab(NULL) + ylab("Relative abundance (%)")+
theme_pubr()+
theme(axis.text.x = element_text(face="bold",family = "TNM",size=20),
axis.text.y = element_text(face="bold",family = "TNM",size=15),
axis.title.y = element_text(face="bold",family = "TNM",size=25))+
theme(legend.position="right",legend.title=element_text(family="TNM",face="bold", size=20))+
theme(legend.text = element_text(size = 13, face="bold",family="TNM"))
phybar
