R-PCA图

作者: 曲凉不见 | 来源:发表于2020-02-13 10:39 被阅读0次

group.B.txt

Sample Group1 Group2
M3N2 Control Meth_7d
M3B2 Control Meth_7d
M3L4 Control Abst_14d
M3N1 Control Meth_0d

1-B_bray_curtis.txt

M1B1 M1B2 M1B3 M1B4 M1L1 M1L2 M1L3 M1L4 M1N1
M1B1 0 0.406891514 0.464991414 0.415630847 0.528281094 0.555857403 0.51824752 0.479445911 0.533112074
M1B2 0.406891514 0 0.378623235 0.355250006 0.530049463 0.426138548 0.37125503 0.410992081 0.570619442
M1B3 0.464991414 0.378623235 0 0.353481637 0.53799431 0.494976806 0.327378969 0.386427125 0.632358595
M1B4 0.415630847 0.355250006 0.353481637 0 0.54327379 0.510866501 0.39643507 0.35325098 0.57880776
M1L1 0.528281094 0.530049463 0.53799431 0.54327379 0 0.555716446 0.553281735 0.5228991 0.518093749
M1L2 0.555857403 0.426138548 0.494976806 0.510866501 0.555716446 0 0.438799047 0.508508675 0.665893539
M1L3 0.51824752 0.37125503 0.327378969 0.39643507 0.553281735 0.438799047 0 0.368858761 0.642802225
M1L4 0.479445911 0.410992081 0.386427125 0.35325098 0.5228991 0.508508675 0.368858761 0 0.565058049
M1N1 0.533112074 0.570619442 0.632358595 0.57880776 0.518093749 0.665893539 0.642802225 0.565058049 0
M1N2 0.449844947 0.433673339 0.55933007 0.465196443 0.479958482 0.612099234 0.50192214 0.492516466 0.452817858
M1N3 0.443463441 0.408582998 0.3720367 0.438606833 0.470065865 0.551782465 0.4882365 0.435185422 0.557190087
M1R2 0.438594018 0.420602783 0.52598734 0.47296189 0.410453881 0.566941746 0.53967298 0.516286937 0.419206028

代码

library(ggplot)
library(vegan)
design<-read.table("group.B.txt",header=T,row.names=1,sep="\t")
data<-read.table("1-B_bray_curtis.txt",sep="\t",header=T,check.names=F)
idx=rownames(design) %in% colnames(data)
sub_design=design[idx,]
data=data[rownames(sub_design),rownames(sub_design)]
pcoa=cmdscale(data,k=3,eig=T)
points=as.data.frame(pcoa\$points)
colnames(points)=c("x","y","z")
eig=pcoa$eig
points=cbind(points,sub_design[match(rownames(points),rownames(sub_design)),])
ggplot(points,aes(x=x,y=y,color=Group2)) +
geom_point(alpha=.7,size=2) +
stat_ellipse(level=0.95,show.legend=F) +
theme(panel.background=element_blank(),panel.border=element_rect(linetype="solid",fill=NA),
axis.text=element_text(size=10,color="black"),axis.title=element_text(size=12,face="bold",color="black")) +
labs(x=paste("PCoA 1 (", format(100 * eig[1] / sum(eig), digits=4), "%)", sep=""),
y=paste("PCoA 2 (", format(100 * eig[2] / sum(eig), digits=4), "%)", sep=""),
title="bray_curtis PCoA")

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