The trans_plot function fails to properly show the full gene structure and strand orientation.

[Jiang-Bio]

Dear Dr. Zhang Jun,

I hope this message finds you well.

-First and foremost, I would like to express my sincere appreciation for your excellent work in developing the R package riboTransVis. It has greatly facilitated the analysis and visualization of our ribosome profiling data, and we are truly grateful for your efforts in advancing tools for epitranscriptomic research.

While using riboTransVis to visualize Ribo-seq data, I encountered an issue regarding the display of gene structures. Specifically, the complete gene model, including untranslated regions (UTRs), was not shown in the output plots as expected (see the example in your package documentation). An example of the issue is attached below:

After reviewing the source code, I found that modifying line 232 in the file visualization-methods.R resolved the issue and produced the desired visualization, including both UTRs and coding sequences. The modification and resulting plot are shown here:

The revised output now clearly displays the full gene structure. However, I noticed that the visualization still lacks strand information for the gene, which would be helpful for interpreting the data in the correct genomic context.

Would it be possible to consider incorporating strand information in a future update? This addition would further enhance the clarity and utility of the package for users working with strand-specific data.

Thank you again for developing and maintaining such a valuable tool. I truly appreciate your time and dedication.

Best regards,
Jiang dingkun
jiangdk_bio@163.com