Tools

Tool Tabs

Select the icon to jump to the relevant section.

Graph Information

Note

Under active development.

Display for graph information.

When a node is selected, information about that node will be displayed here. Icons for each node type:

Segment

Corresponds to S line in GFA.

Bubble

A bubble containing one or more segments.

Note

Debugging information will be displayed here if the instance was started in debug mode.

Path Selector

Tools for viewing paths.

Select a sample to view the paths that are contained in the subgraph currently being viewed. “Show All Paths” will highlight links touched by any path in that sample. Selecting a specific graph can enable animation of it. You can play through the steps of the path using the controls below.

Play

Start playback of the path animation.

Previous

Go back to the previous step.

Next

Advance to the next step.

Pause

Pause the animation at the current step.

Reset

Restart the animation from the beginning.

Gene Annotations

Adjusting annotations.

Each annotation has three options:

• Toggle visibility (by clicking on gene name)

• Draw exons only (by clicking on the icon)

• Change color (by clicking on the color swatch)

Draw exons

When enabled, exons will be drawn on the graph instead of full genes.

Search

Note

More options will be added here over time.

Search features.

Currently this section only supports searching for nodes by ID. Clicking on a search result will center the canvas view on that node.

Settings

Adjust forces and rendering settings.

Charge

Controls the repulsive force applied to nodes.

Charge Distance

Sets the maximum distance over which nodes exert charge force.

Node Collision

Prevents nodes from overlapping by applying collision force.

Collision Radius

The radius around a node that determines a collision.

Link Size

Shrinks or grows target link length.

Friction

Dampens node motion, slowing down layout movement.

Layout Impulse

Applies a force that drives nodes to their initial layout positions.

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Node Width

Adjusts the thickness of node rendering.

Font Size

Changes the annotation label font sizes.

Options

Note

More options will be added here over time.

Miscellaneous options.

Anchor on drag

Fixes a node to a dragged position when enabled.

Smooth GC colors

Smooths out color in GC style by averaging GC content over a node and its neighbors.

Input Commands

Self-explanatory list of input commands.