James Ferguson
@psy-fer
Bioinformatician/Genomics Software Engineer @garvaninstitute.bsky.social Views my own. Mastodon @Psy_Fer_@genomic.social,
So back when the pandemic hit, we were doing the sequencing for contact tracing, and needed a quick way to asses coverage across the amplicon pools. So I made CoVarPlots to do that (img1). I've now ported that across to kuva with some more functionality (img2). Coming in v0.6
kuva v0.5.0 release! - CLI plots that print their own Rust code (--emit-code) - Multi-page PDF export - Fresh docs site - A 64th plot type: Pareto chart - twin-Y axes, date/time X axes, header control (--header), label backgrounds, subtitles - Security update (thanks CDC) github.com/Psy-Fer/kuva
zooid specialisation is up there as one of the coolest things i've ever encountered in biology. Read all about the genomics involved in specialisation and the molecular basis of venom activity in the Bluebottle Physalia Utriculus
Cool new feature for kuva i've been cooking up. So when you use the CLI, you can get a nice plot, but what if you want to now port that over to the library? well, --emit-code will dump the rust code needed to re-produce the same CLI built plot. This will be in the next release :)
no way. I created this repo yesterday and this is my "watch" setting. I think I would still get notified of any issues or PRs because of my global email settings though.
kuva v0.4.0 released Black & white / accessibility mode across all 61 plot types, sharper text layout, and axis dead-space fixes. A big thanks to @tfenne.bsky.social for the great bug reports and PRs this release. github.com/Psy-Fer/kuva
kuva v0.3.0 release! - New raster backend: faster than the old one, dropped dep. - New QuiverPlot type - Pre-compiled release binaries (thanks @wdecoster.bsky.social ) - .parquet input for all CLI subcommands Also lots of fixes and other features crates.io/crates/kuva github.com/Psy-Fer/kuva
going through all the last checks for a new kuva release, and gosh some of the test plots are pretty 😍
lookout, i'm asking the tough questions, to fable, and it's not having it!
Did I mention it's fast? I also added an experimental VBZ-K: generalised K-stream parallel decode method. Though it requires storing the breakpoints in the signal. But basically, it let's you do threading on VBZ decode. A bit fiddly to set up, but goes fast 😎
Iterating through various raster methods for drawing lines for making PNG files generate faster with kuva on very large dataset inputs. Made some good progress. While the polyline-opt method was faster, it's visual fidelity was...ahh...shit. So doesn't count haha
HAHAHAHAHAHAHAAHAHA Love a good chartfail, but this is literally the plotter itself failing.
me: Okay, time to update the png/raster backend of kuva to be faster ... me: aaand done...wait...what? HAHAHAHAHAHAHAHA
In the kuva v0.2.0 update, while I was building the venn diagram plot type, I wanted a way to visually see the overlap group membership that wasn't as ambiguous. So I added these coloured membership dots to help with that. psy-fer.github.io/kuva/plots/v...
kuva v0.2.0 Now over 60 plots! New plot types: Gantt, Network, Waffle, Horizon, PopulationPyramid, Joint, Clustermap, ROC, PR, Lollipop, Survival, Raincloud, Slope, Venn, Parallel, Mosaic, Streamgraph, Radar, Treemap, Sunburst, Bump, Funnel, Rose, Calendar, Legend, Text github.com/Psy-Fer/kuva
Slowly going through all the checks for a new version of kuva to be releases. Probably going to take another few days. But i'm up to 59 plot types now (with lots more sub variants). There is one more plot in a PR, don't worry i'll make it an even 60
And they aren't even using a single brain cell to think about licensing.
After writing my own poa stuff for better consensus calling, this commit was extremely satisfying "yeet the bio crate"
I doubt 1 person can maintain this many repos, effectively, even with LLM assistance. I have to ask the question: "why tho?". Seems like flag planting rather than doing anything useful.
me: I should add some interactivity to my plots also me: *Shoves fully playable DOOM into an SVG file* cargo build --features cli,doom kuva doom -o doom.svg open in browser. that's it. Yes, it's April 1st, but this is real 😅 psy-fer.github.io/kuva/doom.html
Cooking up a cool feature for kuva with --interactive, where it adds a search, and group highlighting and coordinates on mouse, all within the native SVG file, when looking at it with a browser. This is just the minimal working prototype. What do you think?
kuva v0.1.4 released - 4 new plots (Polar, Ternary, Ridgeline, Density) - A completely reworked legend system - SVG rendering 50-70% faster, and Manhattan plots 22× faster at 1M SNPs - Many bug fixes and extra features github.com/Psy-Fer/kuva crates.io/crates/kuva #rust #bioinformatics #dataviz
Made up some ridgeline plots. I think these need a little work still, but i'm happy with this as a baseline
daaamn. Ternary plots are HARD. My brain hurts after getting the basic stuff working. There are so many variants of this plot type 😆 help! Also, new dot feature, with stroke and transparency