Viewing the Pangenome

Node Types

Segments = S lines from GFA files (blue). Links = L lines from GFA files (gray).

A chain of bubbles. Each bubble in the chain is shown in yellow, the chain links are orange.

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

Iterative bubble popping to the segment level.

Gene Annotations

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:

Example of rendered gene annotations.

Interactions

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.

Right-Click Menu

Warning

“Download GFA” is currently broken.

Actions performed on the full subgraph:

Recenter Graph

Zoom to fit the entire subgraph in view.

Download GFA

Export the current subgraph as a GFA file.

Download PNG

Export the current subgraph as a PNG image.

Download SVG

Export the current graph as an SVG vector image.

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Actions performed on a selected set of nodes:

Pop nodes

Pop selected bubbles.

Show Sequence

Display truncated sequence for selected nodes.

Add Custom Label

Assign a custom text label to selected nodes.

Add Custom Annotation

Create a custom gene annotation on selected nodes.

Clear Labels

Remove all custom text labels from nodes.

Unlock nodes

Allow nodes to move freely again.

Lock nodes

Fix node positions to their current coordinates.