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 s...
Blog Archives
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 than...
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...
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, Februa...
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 ot...
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 libra...
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 m...
GWAS Manhattan plots and QQ plots using ggplot2 in R
Will posted earlier this week about how to produce manhattan plots of GWAS results using Stata, so I thought I'd share how I do this in R using ggplot2. First, if you've never used ggplot2, you'll need to add it to your R installation by typing: install.packages("ggplot2") Once you've done that, copy and paste this command to download the functions I wrote...
Coming to R from SQL, Python, SAS, Matlab, or Lisp
Head over to Revolutions Blog for a list of PDF and powerpoint resources for making the transition to R from other programming or stats languages. All of these notes come from the New York R meetup. I enjoyed browsing the meetup's files - lots of powerpoints, PDFs, and example R data files for various topics, including several slideshows on...
ggplot2 Tutorial: Scatterplots in a Series of Small Multiples
It took several months after learning about ggplot2 before I gave it a try myself. I was apprehensive about learning a new graphics system with a new set of commands. Thing is, if you've ever used plot() in R, you already know how to use much of the functionality in ggplot2! In this tutorial I want to show you...
Zero Inflated Models and Generalized Linear Mixed Models with R.
Zuur, Saveliev, Ieno (2012).
