Real-world dataset: Human 27 population data

Step1: running the ipADMIXTURE using Human 27 population dataset where the number of ancestors K =12.

library(ipADMIXTURE)
# # running area: ipADMIXTURE::human27pop_Qmat[[i]] is a Q matrix with K=i+1
h27pop_obj<-ipADMIXTURE(Qmat=ipADMIXTURE::human27pop_Qmat[[11]], admixRatioThs =0.15)

Step2: printing all cluster information in text mode.

ipADMIXTURE::printClustersFromLabels(h27pop_obj,human27pop_labels)

## [1] "Overall labels"
## [1] "==============="
## [1] "Alur(10)Hema(15)Pygmy(25)Brahmin(25)Utah_N._European(25)Cambodian(5)Chinese(10)Tamil_LC(13)Irula(24)JPN2(13)Madiga(10)Mala(11)CEU(60)YRI(60)CHB(45)JPT(45)Luhya(24)Tuscan(25)Kung(13)Pedi(10)Sotho/Tswana(8)Stalskoe(5)Iban(25)TBrahmin(14)Urkarah(18)VN(7)Nguni(9)"
## [1] "==============="
## [1] "ID1, md0.05, N25"
## [1] "Pygmy(25/25)"
## [1] "==============="
## [1] "ID2, md0.13, N56"
## [1] "JPN2(12/13)JPT(44/45)"
## [1] "==============="
## [1] "ID3, md0.00, N12"
## [1] "Kung(12/13)"
## [1] "==============="
## [1] "ID4, md0.00, N25"
## [1] "Iban(25/25)"
## [1] "==============="
## [1] "ID5, md0.00, N69"
## [1] "Cambodian(5/5)Chinese(10/10)JPN2(1/13)CHB(45/45)JPT(1/45)VN(7/7)"
## [1] "==============="
## [1] "ID6, md0.06, N25"
## [1] "Utah_N._European(1/25)Tuscan(24/25)"
## [1] "==============="
## [1] "ID7, md0.09, N85"
## [1] "Utah_N._European(24/25)CEU(60/60)Tuscan(1/25)"
## [1] "==============="
## [1] "ID8, md0.00, N17"
## [1] "Urkarah(17/18)"
## [1] "==============="
## [1] "ID9, md0.00, N6"
## [1] "Stalskoe(5/5)Urkarah(1/18)"
## [1] "==============="
## [1] "ID10, md0.00, N4"
## [1] "Irula(4/24)"
## [1] "==============="
## [1] "ID11, md0.00, N10"
## [1] "Irula(10/24)"
## [1] "==============="
## [1] "ID12, md0.00, N9"
## [1] "Irula(9/24)"
## [1] "==============="
## [1] "ID13, md0.00, N33"
## [1] "Tamil_LC(13/13)Madiga(9/10)Mala(11/11)"
## [1] "==============="
## [1] "ID14, md0.08, N41"
## [1] "Brahmin(25/25)Irula(1/24)Madiga(1/10)TBrahmin(14/14)"
## [1] "==============="
## [1] "ID15, md0.00, N4"
## [1] "Pedi(2/10)Sotho/Tswana(2/8)"
## [1] "==============="
## [1] "ID16, md0.00, N20"
## [1] "Pedi(5/10)Sotho/Tswana(6/8)Nguni(9/9)"
## [1] "==============="
## [1] "ID17, md0.00, N4"
## [1] "Kung(1/13)Pedi(3/10)"
## [1] "==============="
## [1] "ID18, md0.04, N60"
## [1] "YRI(60/60)"
## [1] "==============="
## [1] "ID19, md0.00, N4"
## [1] "Hema(2/15)Luhya(2/24)"
## [1] "==============="
## [1] "ID20, md0.00, N2"
## [1] "Luhya(2/24)"
## [1] "==============="
## [1] "ID21, md0.07, N20"
## [1] "Luhya(20/24)"
## [1] "==============="
## [1] "ID22, md0.12, N23"
## [1] "Alur(10/10)Hema(13/15)"

Step3: plotting admixture ratios and clustering assignment.

ipADMIXTURE::plotAdmixClusters(h27pop_obj)

Step4: plotting clustering information in treemap plot

ipADMIXTURE::plotClusterLeaves(h27pop_obj)

Step4: Inferring phylogenetic tree of clusters based on a list of Q matrices that varies K.

out<-ipADMIXTURE::getPhyloTree(human27pop_Qmat,h27pop_obj$indexClsVec)
plot(out$tree, type = "unrooted")