#個體從新排序
#提取個體
plink --file 72breeds --extract reorder.txt --recode --out 72-reorder --chr-set 29
plink --file 72breeds --keep reorder.txt --chr-set 29 --recode --out 72-reorder
library(LEA)
結(jié)果會生成test.geno文件的數(shù)據(jù).
output = ped2lfmm("72breeds-ro.ped")
使用LEA進(jìn)行structure進(jìn)行分析
obj.snmf = snmf("72breeds-ro.lfmm", K = 1:5, ploidy = 2, entropy = T,
alpha = 100, project = "new")
##R繪制stucture圖(pophelper包)
sfiles <- list.files("structure3",full.names=TRUE)
sfiles
slist <- readQ(sfiles)
slist
lab<- read.delim("lab.txt", header=F,stringsAsFactors=F)
plotQ(slist,imgoutput = "join",
outputfilename="structure2",
imgtype="pdf",
panelspacer =0.05,
height = 0.5,
splabangle = 90,
showindlab=F,
grplab=lab[,1,drop=FALSE],
exportpath=getwd())
plotQ(slist,imgoutput = "join",
outputfilename="structure2",
imgtype="PDF",
panelspacer =0.05,
height = 0.5,
splabangle = 0,
showindlab=F,
grplab=lab[,1,drop=FALSE],
grplabangle = 90,
grplabsize = 1,
grplabheight = 5,
exportpath=getwd())
