I recently started using Just the Docs, an awesome documentation theme for Jekyll. You can find one of my last projects dealing with Nanopore RNA-seq there at microbepore.
I started analyzing sequencing data just over one year ago. In the beginning it was so exciting to finally receive the first reads, do some quality checks and start further analysis, that I didn´t think about reproducibility. I ended up with multiple distinct versions of mapped reads, adapter/quality trimmed reads from scripts using different parameters. It was bad…
So I had to force myself to rethink my workflow, which I will show you (in a simplifed way) in the following.
In my opinion packages are one of the main reasons why R is so successfull. They add a whole new level of functionality and reproducibility and also increase the productivity of every user by reusable R functions, their documentation and sample data.
To get straight to the point: This post is about data manipulation and visualization in R.
Obviously, that is something completely different from my first post and with more content coming up, I have to think about giving the blog a clearer structure 🤔
But for now, it should be fine. As you will definitely see some code during your read, please do not be intimidated! You will not miss the final statement, even if you are not familiar with programming. As some kind of a reminiscence to the previous topic, this post again deals with movies and the development of their duration over the years.
At the beginning of the year, I remember myself staring at the screen, sitting on a bunch of genomic data and thinking:
“Man, it would be really helpful to hover over my data points and check what properties they have…”
As this may seem a bit nerdy, nowadays dynamic content has become quite natural and offers a whole new range of possibilities especially when dealing with large, complex data sets.
Is an animated graph contributing to a better understanding?
From the comments and a related second post it became clear, that this animation was visually appealing, but in no way contributing to a better understanding of the data behind the graph.
So I sat down and thought about requirements for an animated bar chart that can be embedded in a presentation and contribute (maybe) to a better understanding:
