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Figure 4 | BMC Bioinformatics

Figure 4

From: Iterative pruning PCA improves resolution of highly structured populations

Figure 4

ipPCA analysis of HapMap human dataset. A) Consensus subpopulation tree. Each cell contains population labels YRI, CEU, CHB, or JPT. The number of individuals is presented in parentheses next to each label. The number of PCs used for clustering is indicated in parentheses in each cell. The blue cell indicates the pre-processed dataset. Nested datasets containing unresolved structure are in green, while the terminated red cells represent resolved subpopulations. B) Scatter-plots using the first and second principal components (PC1 vs. PC2). Each datum point represents an individual. Each population label is denoted by a separate symbol (see inset). The blue frame contains a scatter-plot of ipPCA iteration 0. Scatter-plot of the nested dataset at iteration 1 is framed in green. Scatter-plots of resolved subpopulations are framed in red. The variation captured by each PC is indicated in parenthesis next to the axis label.

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