We extend our gratitude to a-dna-n for valuable contribution. Several enhancements have been implemented in this update, specifically aligned with the guidelines provided in the original author's README documentation.
- In density plots, splice-junction arcs are shown only as positive values, starting and ending at X=0, with their peaks corresponding to the junction counts. This features is implemented for linear and log Y-axis scales. X=0 is a bit artificial but it's key to understanding the magnitude of each arc independently. This feature allows direct comparisons of splice-junction expression levels to each other and to exon coverage, makes it easier to understand what RNA-seq is trying to tell us. The example shows that it can eliminate the need to filter junctions. (plot_func::plot_density)
- Introns can be shown as if they all have a fixed length, e.g. 250 bp. This is akin to how Trackplot scales exons, with every base of a given type occupying the same space. Because it wasn't trivial to modify the parameters to handle this correctly, this feature is overloaded on the intron-scale option: if it's > 1, it's interpreted as the target genomic length of every intron. (plot_func::init_graph_coords).
- When
--transcripts-to-showis specified, unwanted transcripts are dropped immediately upon reading from the GTF file. Otherwise, their coordinates linger in the alignments and take up precious space (in file/Annotation.py).