Monday I upgraded R on my work desptop, which is running Kubuntu 11.10, and upgraded all of my installed R packages, too. This resulted in the breakage of ggplot2 code that had previously worked.Here's the code, which draws a stacked bar chart: # plot...
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Manhattan plot with simulated data using ggplot2
In an earlier post I discussed how you might approach producing Manhattan plots in R using ggplot2. Several readers had questions about the code samples in the post, and asked if I could post the complete code. I didn't think that would be very helpfu...
Update to “Manhattan plots for SNP marker effects using ggplot2″
In the comments several people have asked about the structure of my data. The structure of my data is such that I have to merge several things together to get the final data assembled, which I think is obscuring how I actually get the Manhattan plot. ...
Manhattan plots for SNP marker effects using ggplot2
At AIPL, we've been posting Manhattan plots of the marker effects for each breed-trait combination with each official release of our genomic predictions. For example, consider the plot of lifetime net merit for Holsteins from the April, 2010 run: Thes...
Manhattan plots for SNP marker effects using ggplot2
At AIPL, we’ve been posting Manhattan plots of the marker effects for each breed-trait combination with each official release of our genomic predictions. For example, consider the plot of lifetime net merit for Holsteins from the April, 2010 run: These … Continue reading →
Zero Inflated Models and Generalized Linear Mixed Models with R.
Zuur, Saveliev, Ieno (2012).
