Today is the one year anniversary of the NYC R Statistical Meetup. Starting as a small group meeting in a crowded conference room, Josh Reich established the meetup as the premiere gathering of data geeks in the tri-state area. Over the past year we have had 10 meetups, and two more ... [Read more...]

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 ... [Read more...]

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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... [Read more...]

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... [Read more...]

The video from John Myles White’s outstanding introductory talk on spatial analysis with R to the NYC R Statistical Meetup is now available in the R video repository, and is also embedded after the jump. I would like to thank John for this fantastic talk, and for those interested ... [Read more...]

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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... [Read more...]

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 ... [Read more...]

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 ... [Read more...]

On December 3, 2009 I presented a brief talk at the NYC R meetup on how to create data visualizations with R using the immensely powerful ggplot2 package. The talk is very light on motivation but heavy on examples, so it may be more useful to those with some R and/or ... [Read more...]

One of R's biggest strengths is its unparalleled graphing capabilities.  Just see any of our previous posts on ggplot2, visualization, or other posts tagged with R. R has several fundamentally different systems for plotting, including base graphics, lattice, and ggplot2.  Furthermore, many add-on packages come with their own functions for ... [Read more...]

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Way back will wrote on this topic.  See his previous post for Stata code for doing this.  Unfortunately the R package that was used to create QQ-plots here has been removed from CRAN, so I wrote my own using ggplot2 and some code I received from Daniel Shriner at NHGRI. ... [Read more...]

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Strict quality control procedures are extremely important for any genome-wide association study.  One of the first steps you should take when running QC on your GWAS is to look for related samples in your dataset.  This does two things for you.  First, you can get an idea of how many ... [Read more...]

One of the nicer things about many statistics packages is the extremely granular control you get over your graphical output.  But I lack the patience to set dozens of command line flags in R, and I'd rather not power the computer by pumping the mouse trying to set all the ... [Read more...]

Inspired by this post (suggested here by the always useful Revolutions blog), I attempted to plot the position of CRAN mirrors on a map taking advantage of the nice R package RgoogleMaps (check the dependencies!). Below the code: library(XML) # downlo... [Read more...]

I guess this is not the number one post I would like to start with on this blog, but I feel the time is right for it (community-wise). I’ll move on to the subject matter in a moment, but first a short intro: This blog is written by Tal ... [Read more...]

As far as I know there are 3 different systems for producing figures in R: (1) base graphics, included with R, (2) the lattice package, and (3) ggplot2, one of the newer plotting systems which is, according to the creator Hadley Wickham, "based on the grammar of graphics, which tries to take the good ... [Read more...]