Blog Archives

Compiling RMarkdown from a Helper R Script

August 6, 2015
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Compiling RMarkdown from a Helper R Script

The problemI was looking for a way to compile an RMarkdown document and have the filename of the resulting PDF or HTML document contain the name of the input data that it processed. That is, if I compiled the analysis.Rmd file, where in that file it di...

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R: single plot with two different y-axes

April 21, 2015
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R: single plot with two different y-axes

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 th...

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R User Group Recap: Heatmaps and Using the caret Package

April 10, 2015
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R User Group Recap: Heatmaps and Using the caret Package

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...

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Using and Abusing Data Visualization: Anscombe’s Quartet and Cheating Bonferroni

February 26, 2015
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Using and Abusing Data Visualization: Anscombe’s Quartet and Cheating Bonferroni

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 Ansco...

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Microbial Genomics: the State of the Art in 2015

February 4, 2015
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Microbial Genomics: the State of the Art in 2015

Current Opinion in Microbiology recently published a special issue in genomics. In an excellent editorial overview, “Genomics: The era of genomically-enabled microbiology”, Neil Hall and Jay Hinton give an overview of the state of the field in micr...

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Microbial Genomics: the State of the Art in 2015

February 4, 2015
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Microbial Genomics: the State of the Art in 2015

Current Opinion in Microbiology recently published a special issue in genomics. In an excellent editorial overview, “Genomics: The era of genomically-enabled microbiology”, Neil Hall and Jay Hinton give an overview of the state of the field in micr...

Read more »

R + ggplot2 Graph Catalog

February 3, 2015
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R + ggplot2 Graph Catalog

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 ma...

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Microbiome Digest Blog

January 20, 2015
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Microbiome Digest Blog

I have a noteworthy blogs tag on this blog that I sort of forgot about, and haven't used in years. But I started reading one recently that's definitely qualified for the distinction.The Microbiome Digest is written by Elisabeth Bik, a scienti...

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Using the microbenchmark package to compare the execution time of R expressions

January 14, 2015
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Using the microbenchmark package to compare the execution time of R expressions

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 micr...

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Importing Illumina BeadArray data into R

December 8, 2014
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Importing Illumina BeadArray data into R

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...

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