MOESM9 of Functional analysis of Plasmodium falciparum subpopulations associated with artemisinin resistance in Cambodia

Additional file 9. Hierarchical clustering of 167 isolates based on the network based stratification method [27]. Interaction network was recovered from STRINGv10 and interaction evidence from all the sources was used. Only top 10% of the interactions were included in the analysis. Similarity matrix was computed using consensus clustering, which was performed by selecting 80% mutated genes and 80% isolates 100 times randomly and iterating NMF clustering 10 times. This similarity matrix was then used to build a dendrogram for all 167 isolates using Euclidean distance matrix and ward minimum variance method in R. Colors for different clusters were assigned by comparison with the hierarchical clustering result based on 21,257 SNPs. The isolates classified in different clusters in two approaches (SNP based and Network based) are pointed with triangles. The colors of the triangles correspond to the hierarchical classification.