It’s plot recreation time! In this post, we’ll look at how we can recreate a plot in R. I thought it might be useful to provide the solution but also to detail the process I went through to get there. We have a FACS plot taken from a BD FACS Aria machine: Briefly, it’s a […]
Tag: Rstats
A Pace Far Different: finding best running pace with R
If you are into running, chances are that you will be chasing your PB (personal best) times. This post is about using R to search for your PBs, and to monitor them over time. Usually runners target four distances for PBs: 5 km, 10 km, half marathon and full marathon. It’s likely that a PB […]
Get Better: R for cell biologists
How can we teach “R for cell biologists” rather than teaching R to cell biologists? I’ve noticed that many R training courses will teach R – regardless of who is taking the course – and leave it to the participants to figure out how they can use R in their own discipline. Often, folks from […]
Exploding, Impacting: looking at bioRxiv preprint view dynamics with R
One of the joys of posting a preprint is seeing that people are viewing, downloading and (hopefully) reading your paper. On bioRxiv you can check out the statistics for your paper in the metrics tab. We posted a preprint recently and it clocked up over 1,000 views in the first day or so. This made […]
King of the Mountain: using R to bag a Strava KOM
One of the best features of Strava is the battle to be King (or Queen) of the Mountain. Originally, in cycling, segments were typically climbs or difficult sections of road, and the simple idea, is who can complete the segment in the quickest time. Hence they would be KOM/QOM, King or Queen of the Mountain. […]
Prehistoric: when do authors preprint their papers?
Previously, I took advantage of a dataset that linked preprints to their published counterparts to look at the fraction of papers in a journal that are preprinted. This linkage can be used to answer other interesting questions. Such as: when do authors preprint their papers relative to submission? And does this differ by journal? There’s […]
Bird’s Eye View: using R to generate inventory maps for lab reagents
This is a rather niche post, but the method can likely be adapted for other use cases. In the lab we have many different cell lines stored in liquid nitrogen. The arrangement is: Ideally, to retrieve the correct vial from the cell store requires a map. We have a FileMaker Pro database of all of […]
Pre Self: what fraction of a journal’s papers are preprinted?
Answering the question of what fraction of a journal’s papers were previously available as a preprint is quite difficult to do. The tricky part is matching preprints (from a number of different servers) with the published output from a journal. The easy matches are those that are directly linked together, the remainder though can be […]
Airy Area: approximating surface area of a cell from a 3D point set
In the spirit of “if it took you a while to find out how to do something, write about it”, I will detail a method to approximate the surface area of a 3D shape. Our application here was finding the surface area of a cell but it can be used on any shape. We start […]
All The Right Friends II: clustering papers using Google Scholar data
In a previous post, I looked at how Google Scholar ranks co-authors. While I had the data available I wondered whether paper authorship could be used in other ways. A few months back, John Cook posted about using Jaccard index and jazz albums. The idea is to look at the players on two jazz albums […]