Visualization

Getting Oriented

1. Main menu. From the File menu, you can open maps, load control maps, see dataset metrics, and export an image. From the Annotations menu, you can load one dimensional and two dimensional features and see them alongside the Hi-C map. From the Bookmarks menu, you can save your location to load it again later.

2. Toolbar. Select chromosomes, switch between Observed, Observed/Expected, Control, and other views, adjust normalization, change the resolution, fine-tune the color range, or go to a specific location in the map.

3. Heat map. This is where the heat maps load. You can pan by grabbing the map with the mouse and moving; double-clicking zooms in. You can also zoom in by holding down ALT key and drawing a box around a region of interest.

4. Mini Map. You can see where you are within a chromosome at any time from the mini map. You can move the transparent square in the mini map to quickly change the main map.

5. Information pane. When the mouse moves over the heat map, the text in the pane is updated with information about the specific Hi-C pixel. When features are loaded on the map, detailed information about them appears here.

Let's see how to load a map next.