Drawing Custom Annotations (Desktop)

Drawing Annotations

We can record the differences we see in the GM12878 and IMR-90 maps.

1. Right click the heat map

2. Select Enable diagonal edge

3. Draw custom hand annotations for the differential loops you see by holding down theshift key and drawing a box

If you make a mistake, you can remove the annotation. Right click when within the box and select Configure feature -> Delete.

Editing Panel Options

You can also configure the annotations (both loaded and custom annotations) by clicking Show Annotation Panel and then the 2D Annotations tab. The current layer is Layer 0.

• You can rename the annotation by typing the box

• Clicking the pencil will make the layer editable (this is useful when you import annotations)

• The eye icon is for selectively turning visibility on and off

• The color box allows you to change the color of all annotations in this layer

• The shaded icon makes the annotation more translucent

• The dotted box artificially enlarges the annotation

• The solid box icon toggles through options for only showing the annotation above or below the diagonal; this is especially useful in VS mode with annotations loaded for different files

• The ellipsis enables a mode whereby not all annotations are painted at the same time; this is useful when there are a very large number of annotations loaded

• The backwards circle undoes the last annotation drawn

• The circle with a slash clears all annotations in this layer

• The mini heat map creates a submap (See the Bonus Submapping section)
• The page with a green arrow allows you to export the annotations to a file on your local computer in the .bedpe human-readable format

• The two pages icon duplicates this layer

• The arrows allow you to move the annotation up and down in the list, and thus affects priority of which annotations are drawn (similar to Photoshop layers)

• The trash icon can deletes this layer