Viewing the Pangenome

Node Types

PangyPlot First displays top-level bubbles. Bubbles can be popped to reveal finer-scale details.

The gene annotations are provided during setup up PangyPlot. The HPRC live instance uses annotations from GENCODE (any GFF3 file can be used).

Annotations are rendered as outlines around nodes and edges:

Pan/Zoom Mode default

Click and drag to pan the view. Use mouse wheel to zoom in and out.

Bubble Pop Mode ctrl key/cmd key

Click nodes to pop bubbles.

Selection Mode shift key

Click nodes to select. Drag to create a selection rectangle.

Recenter on Subgraph space bar

Press the space bar to recenter the view on the full subgraph.

Recenter on Selection up arrow

Press the up arrow key to recenter the view on the selected nodes.

Anchor on Drag F key

Press the F key to toggle whether a node position is fixed after dragging.

The right-click menu is context-sensitive: the available actions depend on what is under the cursor and whether you have a selection.

Right-click a chain to act on it:

Flip Chain

Reverse the orientation of the chain.

Pop All Bubbles

Expand every bubble along the chain.

Add Custom Annotation

Name and label the chain (or the current selection).

With a set of chains highlighted (Shift-drag to select), act on the selection:

Copy Approx Coordinates

Copy the coordinate range spanned by the selection.

Pop Highlighted

Expand every bubble within the selection.

Export GFA

Export the selected region as a GFA file (detail view).

Export GFA + Layout

Export the selected region as a GFA file along with its layout, in odgi and Bandage formats (detail view).