Handling of paths that leave and re-enter the displayed subgraph

[6br]

Hello :) I am very grateful for your tool, but I found some unexpected behavior.

• trackDoubleClick on the last track sometimes fails like this.

• Nodes which are not adjacent are shown as if it is concatenated on the path.

In this figure, the red and green lines seem to be concatenated, but they are not adjacent by observing input JSON's rank, which is generated by vg find -x <xg> -P <path> -c <contexts> from our internal dataset.

{"name":"chr20","mapping":[{"position":{"node_id":22608},"rank":6042},{"position":{"node_id":22623},"rank":6057},{"position":{"node_id":22624},"rank":6058},{"position":{"node_id":22625},"rank":6059},{"position":{"node_id":22626},"rank":6060},{"position":{"node_id":22627},"rank":6061},{"position":{"node_id":22632},"rank":6066},{"position":{"node_id":22633},"rank":6067},{"position":{"node_id":22634},"rank":6068}]}

In the same reason, the scale shown on the path is not correct for green / red path. In my opinion, the link which the both nodes are not adjacent but on the same path had better be a dotted line.

Moreover, I have several requests:

• A callback called on dragging SVG to move left or right of genomic regions.
• Enable to select an arbitrary color on each path.
• Make nodeDoubleClick / trackDoubleClick more general API with callbacks.

Sincerely,

[wolfib]

Hi,

Thanks a lot for your suggestions!

I tried to reproduce the issue with the disappearing graph on double-click of a track, but I wasn't successful. What's the console output when that happens? And what steps exactly are you taking to get there? I noticed that you disabled the display of the "22" track, which is the reference in this example. This might sometimes cause unexpected behaviour.

And for your second point, the non-adjacent red and green paths, I do not really understand you description. English isn't my first language, so I think there's something being lost in translation. What would the expected behaviour be and is there a way for me to reproduce the issue?

[6br]

Thanks for your reply!

In the first point, this is the demonstration of the disappearing graph on double-click of a track. (Google Chrome 63.0) And I also found this issue when I enabled the display of the "22" track.

In the second point, I have made a sketch to describe this issue.

English is not my first language, too. So, to avoid misunderstanding about this problem, I am also trying to make the example to reproduce the issue. I also welcome any questions to make it clear.

[adamnovak]

This might or might not still be an issue; vg now has some support for extracting subgrraphs that the same path visits multiple times, in a way where the paths are renamed apart. I'm not sure if that happens in the way the tube map uses vg, or if the tube map handles it well (especially if it happens to the main path we want to use as the ruler).