Figure 1.
SNP data transformed with PCA and t-SNE 1/2.
On the left is a PCA-plot with the first two components, on the right a t-SNE-plot of the very same data from each data source. Data sources: Panel (a) is from the 1001 genomes project, (b) from the RegMap panel and (c) from hapmap3 r2.
Figure 2.
SNP data transformed with PCA and t-SNE 2/2.
On the left is a PCA-plot with the first two components, on the right a t-SNE-plot of the very same data from each data source. Data sources: Panel (a) from hapmap3 r3 (compare with Fig. 1c) and (b) from the Rice Haplotype Map Project (only wild type where the label information was available).
Table 1.
Dunn's Validity Index and Silhouette Validation Method of the transformed SNP data.
Table 2.
Percent correctly classified with various machine learning methods acting on transformed SNP data.