Methylation and Biomarker Visualizations

Mussel Methylation
Mussel Biomarkers
Published

April 4, 2026

Plan of the Week: March 30 - April 5, 2026

High- level outline for the week. Adjusted daily to reflect progress of the day before

  • Moving forward.

Monday - Catch up on UW-RUA and NWS Poster

Tuesday - UW-RUA, No Science

Wednesday - Biomarker Manuscript

Thursday - Biomarker Manuscript

Friday - NWS Symposium

Saturday - Biomarker Manuscript

Sunday - No Science

Plan of the Day

Granular level task list to accomplish the high- level goal outlined above

  • Keep the methylation analysis moving forward
  • Review biomarker visualizations

Projects Touched Today

  • DNA Methylation
  • Mussel Biomarkers

Progress Notes

  • Returning to the biomarker visualizations in R, not just GIS, I had to review what I had, figure out if it was correct, and adjust what wasn’t.

    • First, reviewing the existing viz, I created many with gt(), this will not render beyond HTML - a thing I did not know until too much Googling put me on the right path. To have tables/ data visualizations render in a Word or PDF, the kable() package has to be used in place of the gt() call that is great for my lab notebook, but not for my outputs. 

    • Shifting to kable() also means a change in syntax that took waaaaaaaay too long - I have gotten into a rhythm with tidy and the html rendering since I add something to my digital notebook more often than adjusting my other work - so I focused on web- based rendering, instead of investigating the differences, this made the whole thing feel really silly.

      • I took the existing code, used the R-Ladies platform that has been a huge help in other work, and compared based on output before fixing, getting CoPilot to help with syntax, and running the new part correctly.

      • After that, I rendered the remaining plots in R before deciding what needed to be adjusted - don’t want to waste time. The tables, in manuscript and supplementary, needed to be reworked, along with the multi-faceted plots for the IBRs. I went to work on those.

      • The base structures are good and can be adjusted once revisions are underway. 

  • For the methylation work, I checked in multiple times throughout the day to ensure my extractions were continuing to run properly.

    • By the end of the day, the extractions were about halfway completed.

Outcomes: Products & Word Count

  • Biomarker Plots: 1 multi-panel
  • Biomarker Tables: 2 tables

Today’s total: 0 words

Monthly total to date: 921 words

Annual total to date: 33,593 words

Annual target total to date: 46,500 words

Next Up: Tomorrow’s Plan

  • Tomorrow is Easter, so I have some cooking and family time ahead.