Visualization of Pairwise and Multilocus Linkage Disequilibrium Structure Using Latent Forests
Figure 1
Comparison of linkage disequilibrium visualization methods applied to the Daly et al. dataset [12].
a) triangular heat map of D′ = LOD with LD blocks computed using Haploview v4.2, b) recombination rates inferred with PHASE v2.1, c) textile plot and d) forest of hierarchical latent class models displayed using Tulip. For each layer l, the median of r2 values (resp. distances) is computed over all pairs of variables having their lowest common ancestor in layer l. The magnified node in subfigured) shows the multilocus linkage disequilibrium measure relative to the latent variable thus highlighted. Dotted lines highlight common trends between the four methods. Association signal is visualized through the length of an edge linking a SNP to an additional node.