.. _visuals:
Viewing the Pangenome
==================================
Node Types
~~~~~~~~~~~~~~~~~~~
.. figure:: ../_images/graph/segments.svg
:alt: segments
:align: center
:width: 100%
Segments = ``S`` lines from GFA files (blue). Links = ``L`` lines from GFA files (gray).
.. figure:: ../_images/graph/bubble_chain.svg
:alt: bubble and chain
:align: center
:width: 100%
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.
.. figure:: ../_images/graph/bubble_pop.svg
:alt: Bubbles in PangyPlot
:width: 100%
:align: center
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:
.. figure:: ../_images/graph/gene_annotation.svg
:alt: gene annotation
:align: center
:width: 800px
Example of rendered gene annotations.
Interactions
~~~~~~~~~~~~~~~~~~~
.. raw:: html
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:
.. raw:: html
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.
Actions performed on a selected set of nodes:
.. raw:: html
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.