Resolution:
## Figure 1.
Scree Plot and Heatmap of Top 20 PCs: The scree plots and heatmaps are presented for the simulated data with no structure
(left), HGDP Africans (middle), NECS (right). The scree plot graphs the natural logarithm
of the eigenvalue (y-axis) versus the component number (x-axis). A kink is not observed
in the scree plot for the simulated data with no population substructure (a). For
the HGDP Africans (b) and the NECS (c) the scree plot identifies a kink at the 5^{th }and 4^{th }PCs, respectively. In the heatmaps, each column is a PC and each row is an individual.
Original PCs are standardized by row and the color intensities correspond to the standardized
value of the PC for each individual (green: higher than average, red: lower average)
and are sorted by the corresponding eigenvalues, and rows are sorted by hierarchical
clustering. While no pattern is found in the heatmap of the simulated example without
population structure, a distinct pattern is observed for the HGDP Africans and the
NECS. The pattern in the HGDP Africans is the most distinct since these populations
are well defined and are very different from each other. The pattern for the NECS
is more subtle because the variability in subjects of European ancestry is much lower
than in Africans. However, one can still observe variability beyond the first 2 principal
components.
Solovieff |