Sankey Plot Overlap Analysis: ChromHMM and MethylSeekR This repository contains Sankey plots analyzing the overlap between ChromHMM and MethylSeekR segmentation for 418 EpiRRs. Each EpiRR's overlap is detailed in a corresponding HTML file named {epirr}_SankeyDiagramReport.html. Overview of Overlap Categories Four categories of overlap between chromatin states (18 types) and methylation states (4 types) are visualized: 1. Global View: Showcases the overall overlap between all chromatin and methylation states. 2. Focused View: Zooms in on the overlap, excluding broad chromatin states such as 5_Tx, 6_Tx_Wk, 13_Het, 17_ReprPCWk, and 18_Quies. 3. LMR Distribution: Compares the distribution of Lowly Methylated Regions (LMRs) defined by MethylSeekR with Chromatin states. 4. UMR Distribution: Compares the distribution of Unmethylated Regions (UMRs) defined by MethylSeekR with Chromatin states. Analysis Details - Unit of Measurement: Base pair. - Methodology: Overlaps are calculated by intersecting 200 bp intervals from ChromHMM output with methylation-specific states from MethylSeekR. Interactive Features Interactive plots enhance user engagement: - Y-axis: Displays genomic coverage in base pairs. - Cursor Interaction: Reveals specific overlap details in base pairs for each state upon hovering over the strata/flow. contact : Abdulrahman Salhab