R-PCA图

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

R-PCA图
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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")