Fig. 1

Mouse full-stack state emission parameters. A Each of the 100 rows in the heatmap corresponds to a mouse full-stack state. Each of the 901 columns corresponds to one input dataset. For each state and each dataset, the heatmap gives the probability within the state of observing a binary present call for the dataset’s signal. Above the heatmap, the first color bar indicates the assay/chromatin mark measured by each dataset. The second color bar shows the cell type groups associated with each dataset. The corresponding color legends are shown towards the bottom. The states are displayed in 16 groups based on biological interpretations indicated by the color legend at the bottom, with white space between each group. Full characterization of states is available in Additional file 2. The model’s transition parameters between states can be found in Additional file 1: Fig. S1. Columns are ordered such that datasets profiling the same chromatin marks are next to each other. B Each row corresponds to a full-stack state as ordered in A. The columns correspond to the top 10 datasets with the highest emission value for each state, in order of decreasing ranks, colored by their associated chromatin marks as in A. C Similar to B, but datasets are colored by the associated cell type groups. The cell type groups primarily associated with some of the enhancer states are noted inside the heatmap. A fully annotated version of Fig. 2B–C is provided in Additional file 3