junction arc line and --included-junctions problem

[tianwen0003]

Dear ygidtu,

I encountered two issues while generating Sashimi plots using trackplot.

In trackplot v0.5.3, the junction arcs are positioned much closer to the x-axis compared to v0.5.1, making it difficult to clearly distinguish the start and end points of each arc.

When using the --included-junctions parameter to display only the junctions of interest (based on coordinates reported by LeafCutter, e.g., chr16:89724829-89726948 in my dataset), the expected junctions were not displayed. Could you please provide a more detailed explanation of the coordinate system used by trackplot in the tutorials?

I have attached the data and code used to reproduce these issues. I look forward to your reply.

trackplot_issue.zip

[ygidtu]

Hi, The plotting logic for junctions got corrupted during the merge, so I reverted it to v0.5.1. Please pull the latest code and retry. Yiming zhang

[tianwen0003]

Thanks for your prompt and effective response — the issue with the junction arc line has been resolved. Regarding the intron coordinates reported by LeafCutter, adding +1 to the upstream intron start allows the --included-junctions parameter to work correctly. In other words, changing chr16:89724829-89726948 to chr16:89724830-89726948 resolves the problem.

[ygidtu]

Hi, Thank you for the feedback. In the original design, logs are displayed only in --verbose mode. In v0.5.5, I’ve added a coordinate comparison during junction processing and introduced a warning message to alert users about 1-bp mismatched junctions.

Best, Yiming Zhang