ipADMIXTURE_demo"

In ipADMIXTURE: Iterative Pruning Population Admixture Inference Framework

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)

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")

ipADMIXTURE documentation built on March 26, 2020, 7:38 p.m.