I forgot where I originally found the code to do this, but I recently had to dig it out again to remind myself how to draw two different y axes on the same plot to show the values of two different features of the data. This is somewhat distinct from the typical use case of aesthetic mappings in ggplot2...
At our most recent R user group meeting we were delighted to have presentations from Mark Lawson and Steve Hoang, both bioinformaticians at Hemoshear. All of the code used in both demos is in our Meetup’s GitHub repo.Making heatmaps in RSteve started with an overview of making heatmaps in R. Using the iris dataset, Steve demonstrated...
Anscombe’s quartet comprises four datasets that have nearly identical simple statistical properties, yet appear very different when graphed. Each dataset consists of eleven (x,y) points. They were constructed in 1973 by the statistician Francis Anscombe to demonstrate both the importance of graphing data before analyzing it and the effect of outliers on statistical properties.Let’s load and view...
Joanna Zhao’s and Jenny Bryan’s R graph catalog is meant to be a complement to the physical book, Creating More Effective Graphs, but it’s a really nice gallery in its own right. The catalog shows a series of different data visualizations, all made with R and ggplot2. Click on any of the plots and you get the...
I recently learned about the microbenchmark package while browsing through Hadley’s advanced R programming book. I’ve done some quick benchmarking using system.time() in a for loop and taking the average, but the microbenchmark function in the microbenchmark package makes this much easier. Hadley gives the example of taking the square root of a vector using the built-in...
A colleague needed some help getting Illumina BeadArray gene expression data loaded into R for data analysis with limma. Hopefully whoever ran your arrays can export the data as text files formatted as described in the code below. If so, you can import...
Last week I ran a one-day workshop on RNA-seq data analysis in the UVA Health Sciences Library. I set up an AWS public EC2 image with all the necessary software installed. Participants logged into AWS, launched the image, and we kicked off the morning ...
I talked a little bit about tidy data my recent post about dplyr, but you should really go check out Hadley’s paper on the subject. R expects inputs to data analysis procedures to be in a tidy format, but the model output objects that you get back aren’t always tidy. The reshape2, tidyr, and dplyr are meant to...
TL;DR? We started an R Users group, awesome community, huge turnout at first meeting, lots of potential.---I've sat through many hours of meetings where faculty lament the fact that their trainees (and the faculty themselves!) are woefully ill-prepared...
Data “janitor-work” The New York Times recently ran a piece on wrangling and cleaning data: “For Big-Data Scientists, ‘Janitor Work’ Is Key Hurdle to Insights” Whether you call it “janitor-work,” wrangling/munging, cleaning/cleansing/scrubbing, tidying, or something else, the article above is worth a read (even though it implicitly denigrates the important work that your housekeeping staff does). It’s...
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