Fix: Reduce overlap of junction numbers under high-density conditions

Improvements & Fixes

Better Junction Label Placement

We've improved how junction numbers are displayed in areas with dense road networks or complex intersections.

What's changed:

• Previously, when multiple junctions were located very close to each other, their labels (numbers) would often overlap, making them unreadable.
• This update introduces smarter label collision detection and spacing logic.

What's better now:

• Labels are automatically repositioned or adjusted to maintain clarity, even in complex areas.

Bugfix release: Fix Y-axis alignment and boundary issues in plotting module

Full Changelog: v0.5.8...v0.6.0

Better visualization with --same-y

We've fixed a long-standing issue with the --same-y parameter in trackplot.

What's changed?

• When --same-y is enabled, all panels now correctly share the same global y-axis range (min/max across all panels).

Why it matters?

• Previously, if junction expression levels varied greatly across panels, some junctions would get "squashed" against the x‑axis, making them nearly invisible.
• Now the y‑axis scaling is truly consistent, so all junctions are displayed with proper height proportions—no more hidden signals at the bottom.

Impact: More reliable and publication‑ready multi‑panel visualizations.

v0.5.9

What's Changed

• optimize the code by ruff format and isort
• add precompute y limits to make sure the proper junction and density layout
• optimize CLI: lazy server import + refactor process_file_list by @zhou-ran in #105
• Optimize/cli lazy import by @zhou-ran in #106
• Fix junction arcs clipped with same-y by @zhou-ran in #108

Full Changelog: v0.5.7...v0.5.9

Fix junction arcs are cutted off sometimes when using --same-y

Problem: Under the --same-y configuration, certain junction arcs may be incorrectly clipped.

Fix: Adjust the arc rendering logic to preserve the full geometry. Thanks to @christophrippl for reporting the issue.

v0..5.7 bug fix

Full Changelog: v0.5.6...v0.5.7

1. fix include junctions
2. add --show-mean-junction-num to better control the junction number display while merging bam files

v0.5.3 fix serval bugs, add new feature to intron scaling

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-show is 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).

v0.5.2 fix transcript_id and transcript_name issues

Fix a minor bug where the transcriptid cannot be displayed when the transcriptname doesn't exist in the gtf or gff file.

v0.4.0 fix interval issues

fix intervals loading and plotting

v0.3.8 compatible with adjustText > 1

1. compatible with adjustText > 1
2. update requirements

v0.3.7 update requirements and fix annotation in web

1. update requirements to security alerts
2. fix annotation in web

Full Changelog: v0.3.6...v0.3.7