Figure 1.

The 4 diagonal matrices (3D rep1 and rep2, 2D rep1 and rep2) are the heatmaps that show the norms of portions of the Hi-C matrices after RPM (A) and ICE (B) application, after the centromeres are removed. Each pixel within these heatmaps represents a summary of an interaction between 2 chromosomes; each is obtained by taking the norm of the corresponding block from the Hi-C matrix and dividing by the length of the corresponding chromosomes. On the off-diagonal, the heatmaps show the absolute magnitude difference between the diagonal heatmaps, all on the same scale, so that these matrices are symmetric about the diagonal matrices. Color bars shown right of both (A) and (B) correspond to individual matrix diagonal values. Color bars shown below (A) and (B) correspond to individual matrix off-diagonal values. Note that the difference between replicates is relatively small compared to the difference between growth conditions.