Insertion-avoiding reads can be confusing to look at

[adamnovak]

I was sent this example paper figure made with the tube map:

Figure 3. SequenceTubeMap graph layout for the same 98bp insertion in chr14 for the COLO828 Tumor cell-line. The sequence graph illustration shows both the inserted sequence and the reads supporting the inserted haplotype along with the reference.

It wasn't clear to the viewer what-all was going on, or what the different lines and the node boxes represented.

It also was not clear what the reads at the bottom, under the nodes and away from the haplotypes they follow, are doing there. Since they are bright and visually prominent, seeming to come toward the viewer, it looks like they might have some sequence associated with them, or otherwise have something to do with the insertion being described. Instead, that part of those reads represents no sequence.

It would be better if the reads not taking the insertion could run parallel to/along with the reference path somehow, or at least look less like they are doing something exciting.

[olivewong]

Legend mockup with meanings for symbols Other ideas for making visualization clearer:

• Make everything grey that's not in a node to show that these reads do not visit the node
• Make haplotypes and reference more prominent/contrasting (by default, reference is similar light blue as some reads)
• Include small examples to explain tube map language (like in the paper, illustrated help)
• Maybe add an about link, or one line explanation of the site