For the overlap enrichment plots in the figures, the enrichments for each genomic feature (column) across all states is normalized by subtracting the minimum value from the column and then dividing by the max of the column. So the values always range from 0 (white) to 1 (dark blue) i.e. its a column wise relative scale. For the neighborhood positional enrichment plots, the normalization is done across all columns i.e. the minimum value over the entire matrix is subtracted from each value and divided by the maximum over the entire matrix.
