Plots of Ancestry estimates

We provide two types of plots of $\hat Q$ (the estimated membership coefficients for each individual, in each cluster. The first representation comes up automatically when you click on the corresponding run in the left-hand window. Each individual in the data set is represented by a single vertical line, which is partitioned into $K$ colored segments that represent that individual's estimated membership fraction in each of the $K$ inferred clusters.

Figure 9: Summary plot of estimates of $Q$. Each individual is represented by a single vertical line broken into $K$ colored segments, with lengths proportional to each of the $K$ inferred clusters. The numbers (1..4) correspond to the predefined populations.

The second representation of the ancestry of individuals plots everybody into a triangle (Figure 10). This type of plot is useful for visualizing the data for $K=3$ (Pritchard et al., 2000a). It is kind of a fun tool for exploring higher-dimensional data, but the bar plots are usually easier to interpret.

Figure 10: The triangle plot of $Q$. Each individual is represented by a colored point. The colors correspond to the prior population labels. The estimated ancestry vector for an individual consists of $K$ components which add up to 1. When $K=3$, the ancestry vectors can be plotted onto a triangle, as shown. For a given point, each of the three components is given by the distance to one edge of the triangle. Individuals who are in one of the corners are therefore assigned completely to one population or another. For $K>3$, we represent the data by allowing the user to pick out two of the inferred clusters at a time, and then grouping all the other clusters together.