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 […]
Category: adventures in code
Tips from the Blog XVII: better Process Folder template in Fiji
The Process_Folder template in Fiji is a wonderful thing. It’s the starting point of most of the ImageJ macros that we use in the lab. However, it has a problem. This post is about how to fix it. tl;dr use this gist instead of the built-in template. The Process_Folder template If you’re reading this, you […]
Tips from the Blog XVI: getting FASTA sequences
I am having some fun running AlphaPulldown on a computing cluster. A requirement is to have input sequences in FASTA format. I found that I needed to get ~600 sequences. I had a list of the relevant Uniprot IDs. Surely getting the sequences for these proteins should be straightforward? Solution The Uniprot IDs can be […]
Tips From The Blog XIX: initialising a new RStudio project
I like to set up a standardised directory structure for RStudio projects. The idea came from here. In brief, the structure is: My typical workflow is therefore to: So far, so good. However, this process is a bit tedious. I find it irritating to open up RStudio (which opens up a previous project by default) […]
Over and Over: quick ways to reuse handy shell one-liners
There are a few one-liners that I use in the shell to do some really nifty stuff. I struggle to quickly find and reuse these and asked for a solution on Mastodon. A handy one-liner might be something like (taken from here): This converts all the flac files in subfolders into mp3 files. Obviously, we […]
Twitcher II: tweet frequency and top tweets
Another post looking at Twitter data in R. It follows this one and this one. I wanted to look again at my tweeting frequency over the 12 years on Twitter, but this time do it in a calendar view. Something like a GitHub commit calendar would be perfect. I have used a library for this […]
Any Time At All: tweet frequency around the clock
Please consider this a “supplementary analysis” to my previous post looking at the frequency of tweets from my personal account over the last 12 years. I was curious about what times I was active on Twitter (measured by when I tweeted). Others might be interested in a solution to look at this in R. The […]
Twitcher: tweet frequency over the years
At the time of writing, I have essentially left Twitter. It was a fun ride and without going into what’s happening there now, this is a good opportunity to look at my 12 years on the platform. Early in November, I downloaded my data and locked my Twitter account. This gave me all the data […]
The Package: learning how to build an R package
I recently made my first R package and was asked how I did it. The answer of course was: I searched, read, and stumbled around until it was done. But having gone through the process I figured it was worthwhile summarising what I did and what I found tricky. First off, there are a ton […]
In Circles: fitting a circle to a curve
A comment from a referee led me to find a method to describe curvature of membranes. This is a quick write-up of our solution. I couldn’t find a solution readily available in Fiji, so I created one using a combination of Fiji for tracing the curvature and IgorPro to do the fitting. If there is […]