Publications by Stephen Turner
Fluctuation plot using ggplot2 in R
Found this nice way to visually summarize contingency tables using ggplot2 in R on Hadley Wickham’s ggplot2 cheat sheet. Using the same data in my previous post on making scatterplots in small multiples, I’ll demonstrate how to use ggfluctuation() to make a fluctuation plot. For a two-dimensional table, this simply puts different ...
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Regression Modeling Strategies Course by Frank Harrell
Frank Harrell is teaching his 3-session short course on regression modeling strategies using R here at Vanderbilt next month. Frank is a professor and chair of the Vanderbilt Biostatistics Department, and the author of several massively popular R libraries, including Design, rms, and the indispensable Hmisc. He has also written a bo...
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LocusZoom: Plot regional association results from GWAS
Update Friday, May 14, 2010: See this newer post on LocusZoom. If you caught Cristen Willer’s seminar here a few weeks ago you saw several beautiful figures in the style of a manhattan plot, but zoomed in around a region of interest, with several other useful information overlays. Click to take a look at this plot below, showing t...
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Seminar: Statistical Methods for DNA Resequencing Analysis in Disease-Gene Studies
Department of Biostatistics Seminar/Workshop Series: Statistical Methods for DNA Resequencing Analysis in Disease-Gene Studies Wenyi Wang, Ph.D., Faculty Candidate Stanford Genome Technology Center, UC Berkeley Statistics 2:00-3:00pm Monday, February 15, 2010 MRB III Room 1220 Intended Audience: Persons interested in applied stat...
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Happy Birthday GGD! The 10 Most Popular Posts Since GGD’s Launch
The first post on Getting Genetics Done was one year ago today. To celebrate, here are the top 10 most viewed posts since GGD launched last year. Incidentally, nine of the ten are tutorials on how to do something in R. Thanks to all the readers and all the commenters for sharing your thoughts! ggplot2 Tutorial: Scatterplots in a Ser...
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Arrange multiple ggplot2 plots in the same image window
In a previous tutorial I showed you how to create plots faceted by the level of a third variable using ggplot2. A commenter asked about using faceted plots and viewports and reminded me of this function I found in the ggplot2 Google group. The arrange function below is similar to using par(mfrow=c(r,c)) in base graphics to put more th...
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Create annotated GWAS manhattan plots using ggplot2 in R
A few months ago I showed you in this post how to use some code I wrote to produce manhattan plots in R using ggplot2. The qqman() function I described in the previous post actually calls another function, manhattan(), which has a few options you can set. I recently had to update this function to allow me to color code SNPs of interes...
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Video: ggplot2 Creator Hadley Wickham’s Short Course on Data Visualization Using R
Hadley Wickham, creator of ggplot2, has posted a 2 hour video on data visualization using R. You can find links to the videos and slides over at Revolutions Blog. Check back here soon. I am working with Hadley to arrange a day-long ggplot2 short course here at Vanderbilt this summer. I’ll post the date and registration info once ev...
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Frank Harrell’s Regression Modeling Strategies Course Handouts
The previously mentioned Regression Modeling Strategies short course taught by Frank Harrell is nearly over. Here are the handouts (PDF) from the course. Keep an eye out here, I’ll be writing a few more posts in the near future on topics Frank covered in this course. Related To leave a comment for the author, please follow the l...
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ProbABEL – R package for GWAS data imputation
I’ve been using GenABEL for some time now for GWAS analysis using related individuals. It has an excellent set of functions for estimating a kinship matrix from a dense marker panel and then using this in a linear mixed effects model to allow for related individuals in the analysis of a quantitative trait. GenABEL also has many othe...
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