Kari Lavikka

see you in 1 hour! #BioVis #DataVis meetup

Congrats for the great work!

Parquet and Arrow are great columnar formats, but the abysmal performance of TextDecoder on Chrome (or maybe V8) completely kills any speed benefits when files contain lots of short, unique strings. Even #JavaScript CSV parsers are faster. It’s fine if you don’t need to access the string columns 🤷

JavaScript broke the web (and called it progress) We replaced simple websites with complex apps nobody asked for. Now it takes a complex build pipeline just to change a headline.

Checks out:

www.jonoalderson.com/conjecture/j...

Selections can also drive filtering and aggregation, though the code is still entirely CPU-based for now. I’d like to explore columnar and GPU-based approaches in the future. (2/2)

It’s been a bit quiet on the GenomeSpy front, but I finally had time to implement interval selections and other fancy features. Vega-Lite–style conditional encodings are compiled into shader code, with selection tests running on the GPU—making interactions snappy. (1/2)

I've typically used R (with tidyverse) for analyses, but recently I've been familiarizing myself with Python. Pandas feels quite awkward to me, at least compared to dplyr. But @pola.rs is great! It works wonderfully with Parquet files too. ❤️

Thanks for your kind words! lesson learned! 😅 I'm glad you found my work interesting!

However, I didn’t realize that "Jellyfish," the tool that generates these plots, is not. This is embarrassing.

Dang. My bad. 😬 I'm the first author of this paper and should have ensured the tool's name was unique. The article is about "Jellyfish plots," which depict tumor evolution. We named them that because they resemble jellyfish with their bells and tentacles—and "jellyfish plot" was unique.

Finally, I'm grateful to all the collaborators and supervisors on this and the previous tumor evolution papers and the whole tumor evolution team! (7/7)

GitHub - HautaniemiLab/jellyfish: Jellyfish Plotter for tumor evolution visualization Jellyfish Plotter for tumor evolution visualization - HautaniemiLab/jellyfish

Jellyfish and Jellyfisher are available on GitHub: github.com/HautaniemiLa..., github.com/HautaniemiLa... (docs: hautaniemilab.github.io/jellyfisher/) #OpenSource #RStats #Bioinformatics (6/7)

BioVis on X: "Big congrats to @KariLavikka, Ilari Maarala, @jaanaoikkonen, Yilin Li, Alexandra Lahtinen, @Sampsa_H on their best abstract award at #BioVis at #ISMBECCB2023 for "Visualizing temporal and multi-regional evolution of tumor subclones with Jellyfish plots". https://t.co/e0laGVreOt" / X Big congrats to @KariLavikka, Ilari Maarala, @jaanaoikkonen, Yilin Li, Alexandra Lahtinen, @Sampsa_H on their best abstract award at #BioVis at #ISMBECCB2023 for "Visualizing temporal and multi-regional evolution of tumor subclones with Jellyfish plots". https://t.co/e0laGVreOt

Jellyfish won the Best Abstract Award at @BioVis at ISMB/ECCB 2023! 🏆 x.com/biovis_net/s.... It took a while to wrap up this project, but I'm happy it's now published—this paper will also be the third and final publication in my PhD dissertation! (5/7)

Jellyfish automates the drawing process and generates visually pleasing plots with ease. Based on the data used in the tumor evolution paper, we've now made auto-generated, interactive Jellyfish plots available at hautaniemilab.github.io/jellyfish/ (4/7)

Evolutionary states and trajectories characterized by distinct pathways stratify patients with ovarian high grade serous carcinoma Ovarian high-grade serous carcinoma (HGSC) is typically diagnosed at an advanced stage, with multiple genetically heterogeneous clones existing in the…

The Jellyfish visualization design was initially published in our paper on tumor evolution in ovarian high-grade serous carcinoma (Lahtinen, Lavikka, Virtanen, et al., 2023, www.sciencedirect.com/science/arti...). However, in that paper, all Jellyfish plots were drawn manually. (3/7)

Metastases in solid tumors consist of heterogeneous subclonal mixtures that evolve across space and time. Jellyfish integrates tumor phylogeny and subclonal compositions of spatiotemporal samples into a unified plot, making subclonal dynamics easier to interpret. #CancerResearch (2/7)

Jellyfish: integrative visualization of spatio-temporal tumor evolution and clonal dynamics AbstractSummary. Spatial and temporal intra-tumor heterogeneity drives tumor evolution and therapy resistance. Existing visualization tools often fail to c

Jellyfish visualization tool and the Jellyfisher R package have now been published in OUP Bioinformatics! 🎉 doi.org/10.1093/bioi... #Bioinformatics #DataViz (1/7)

jellyfisher: Visualize Spatiotemporal Tumor Evolution with Jellyfish Plots Generates interactive Jellyfish plots to visualize spatiotemporal tumor evolution by integrating sample and phylogenetic trees into a unified plot. This approach provides an intuitive way to analyze t...

Thrilled to announce that my R package 'jellyfisher' is now available on CRAN! It's my first package submission to CRAN, and a related paper will (hopefully) be published soon. Check it out: cran.r-project.org/web/packages....

Congrats!

It's not weird. It's relaxing. I've been doing the same.

Announcement online meetup: A picture of health: Visualisations in medical publishing. Showing logo of BioVis community, a stylized bar chart, and a picture of the speaker.

🚨 next #BioVis #Dataviz virtual meetup:

Will Stahl-Timmins (The #BMJ) is joining us on Sept 18!
"A picture of health: Visualisations in medical publishing"

Details & Link:
biovis.net/2024/meetup/

Deciphering cancer genomes with GenomeSpy: a grammar-based visualization toolkit AbstractBackground. Visualization is an indispensable facet of genomic data analysis. Despite the abundance of specialized visualization tools, there remai

My first first-author paper is now published: doi.org/10.1093/giga.... GenomeSpy is a grammar-based visualization toolkit for genomic data, powered by efficient WebGL rendering. Check the paper for examples on how we use it to explore a large ovarian high-grade serous carcinoma dataset.