Hey folks, If you’ve watched any of my livestreams when someone asks why I don’t get ChatGPT or something to do a task for me, you probably saw a pained expression come across my face. Part of me dies every time someone tells me that they used some LLM chatbot to solve a problem. I have many reasons for despising the fascination with AI-based tools. I even wrote a commentary that I submitted to mBio in the fall of 2024. Yes, I wrote it. By hand. Then I typed it. No really, I typed it on a...
14 days ago • 3 min read
Hey folks, It has been great to see the high level of engagement with my weekly critique videos on YouTube. I have really enjoyed making them and have learned a lot about current practices in data visualization. The one problem with these videos is that they’re a bit like an autopsy. We can figure out what went well or what didn’t work in a published figure. But we can’t do much to improve the published figure. What if we could do critiques before submitting our papers, preparing a...
20 days ago • 6 min read
Hey folks, This week I want to share with you a figure that resembles many a type of figure that I see in a lot of genomics papers. I’d consider it a data visualization meme - kind of like how you’re “required” to have a stacked bar plot if you’re doing microbiome research or a dynamite plot if you’re publishing in Nature :) This figure was included in the paper, “Impact of intensive control on malaria population genomics under elimination settings in Southeast Asia” that was published...
27 days ago • 4 min read
Hey folks! I hope you enjoyed last week’s series on the radial volcano plot (newsletter, critique video, livestream). I think it did a good job of illustrating the various reasons I think it’s valuable to recreate figures, even if we don’t like how they display the data. Something I didn’t really emphasize in last week’s newsletter was that by recreating a figure, we can make sure that the data are legit. I’m surprised by the number of signals I’ve been finding where authors using tools like...
about 1 month ago • 3 min read
Hey folks! Before launching into this week’s visualization, I’m looking for a bit of feedback. Since November, I’ve settled into a new routine with this newsletter and the YouTube channel. Each week this newsletter introduces a visualization at a 30,000 ft view or discusses a specific topic in some depth (example). The following Monday I post a video critiquing the visualization (example). Then on Wednesday (or Tuesday like this past week), I livestream a video where I recreate the...
about 1 month ago • 5 min read
Hey folks! I just got back from a seminar. I’m still trying to stretch out my eyes from straining to see the small text on each slide! If you don’t know why I’m brining this up, then you must have missed the videos I posted earlier this week. I was discussing the factors we should consider when converting figures designed for papers to figures designed to a slide deck. You can see me critique a figure from my own lab here and the livestream where I refactor the figure can be found here. I’d...
about 2 months ago • 5 min read
Hey folks, I was a student-invited speaker at the Syracuse University Biology department this week. It was great to meet with them and hear how they are benefiting from these newsletters and my videos. As much as I love posting newsletters and videos, seeing people light up at ideas, laugh at my jokes, and tell me how they are using what I teach them is like jet fuel. I actually gave two talks. One talk covered what I’ve learned about data visualization by critiquing, recreating, and remaking...
about 2 months ago • 5 min read
Hey folks, If you missed Wednesday’s livestream, I encourage you to go back and check it out. I recreated a panel from a paper published in Nature that is pretty typical. It was made up entirely of photographs. Sometimes I feel like I’m the only PI that doesn’t merge panels into figures using Illustrator or Powerpoint. I prefer to use R with some help from {cowplot} or {patchwork} to do this for me. That way I can write a single script to generate the entire set of panels. The result is a...
2 months ago • 4 min read
Hey folks, This week I’ve been teaching one of my 3 day R workshops as part of my official teaching duties at the U of Michigan. I really enjoy teaching these classes! I offer recorded versions of these workshops that use microbiome data or other types of data to help motivate my teaching of R’s tidyverse packages. If you would like to purchase your own version of these workshop click on those links! Also, if you would like me to teach a live workshop to your group, reply to this email and...
2 months ago • 4 min read
