July 2021 feature set - Githubissues

higlass / higlass-transcripts

Gene transcripts track for HiGlass

MIT License

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July 2021 feature set #8

Closed alexpreynolds closed 10 months ago

alexpreynolds commented 3 years ago

UCSC genome browser-like annotation block style
UCSC genome browser-like intron, exon, 5'UTR, 3'UTR feature count labeling
Boxplot (Tukey box-and-whisker) annotation block style
Color applied from BED12 annotation field (unless overwritten by user-specified options, or unspecified and determined by strand, if available)
Canonical or APPRIS isoform highlight flag and color options
Improved PNG/SVG export for all blockStyle modes
Can now specify maximum row rendering for constrained device viewport (i.e., mobile)

Some example animations of block style modifications:

Feature counts and custom coloring:

Screen Recording 2021-07-14 at 4 13 41 PM

UCSC genome browser-like block style:

Screen Recording 2021-07-14 at 4 20 44 PM

Tukey boxplot block style:

Screen Recording 2021-07-14 at 4 24 20 PM

Canonical isoform highlighting:

alexpreynolds commented 3 years ago

Just wanted to check in on this.

alexander-veit commented 3 years ago

I will have a look today. Sorry it took so long.

alexpreynolds commented 3 years ago

Thanks — will work through these and follow up.

alexpreynolds commented 3 years ago

I think I resolved the concerns outlined here, except for the question about how to get the "current" higlass container.

I may add some more commits from performance testing, as it does a bit more work than the generic gene annotations track and so slows down rendering a bit more than we were hoping.

Still, if there are any outstanding issues with what is there currently, please let me know!

alexander-veit commented 2 years ago

I am having some issues with the latest changes. Amino acids are not shown anymore when zoomed in and transcripts vanish occasionally when zooming. See here: https://gyazo.com/1a0e0d138845384ed4bce6b3c05088d0

alexpreynolds commented 2 years ago

I'm not entirely sure what to look for. Do you have a viewconf I can use to try to replicate this locally?

alexander-veit commented 2 years ago

You are not seeing the flickering issue locally? I used the transcript track configuration from https://higlass.io/app/?config=Yzld015XRFaCfCIYbB2MZQ

Edit: but you are seeing the issue in the gif above, right?

alexpreynolds commented 2 years ago

I'll try to set up a site to load your viewconf to try to reproduce things locally.

I did not see flickering in the GIF you posted. It otherwise looks normal to me, but the amino acid view is not my typical use case.

Is there an easy way to repeat the same animation, but with the stock version of the plugin ("expected" vs "observed")? If not, that's fine.