As many of you will be aware, I like to post some R code, and I especially like to post base R versions of ggplot2 things! Well these amazing boxplots turned up on github – go and check them out! So I did my own version in base R – check out ... [Read more...]

Reading data from google sheets into R is something you imagine should be really simple, but often is anything but. However, package googlesheets goes a long way to solving this problem. Let’s crack on with an example. First, install the software: install.packages("googlesheets") We then need an example ... [Read more...]

You have a matrix in R, and you want to visualise it – say, for example, with each cell coloured according to the value in the cell.  Not a heatmap, per se, as that requires clustering; just a simple, visual image. Well, the answer is image() – however, there is the slightly ... [Read more...]

I came across a really cool tweet a few days ago containing an animated GIF demonstrating rise in global temperatures since 1880: Visualizing the Warmest August in 136 Years https://t.co/PSjA2NfYem Data via @NASAGISS #NASA #climate pic.twitter.com/DIk8z7Zodj — NASA Earth (@NASAEarth) September 12, 2016 Link to the ... [Read more...]

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Very quick one this!  Really interesting paper from Ioannidis et al about citation indices. I wanted to recreate figure 1, which is: Closest I could get (code here) is this: Biggest difference is in NS, where they find all negative correlations, but most of mine are positive. Source data are Table ... [Read more...]

Due to the unspeakable horror of the EU referendum, I have to find something to make me feel better.  This poll of polls usually does so, though it is way too close for comfort. Anyway, I took their data and plotted it for myself.  Data and script are on github, ... [Read more...]

Use of the Pearson correlation co-efficient is common in genomics and bioinformatics, which is OK as it goes (I have used it extensively myself), but it has some major drawbacks – the major one being that Pearson can produce large coefficients in the presence of very large measurements. This is best ... [Read more...]

If you have MiSeq and ONT MinION data, it is now very easy to combine them into a single-contig, high quality assembly.  Here I will start with a base Ubuntu 14.04 LTS distribution and take you through every step, including software installation.  I am starting with an Amazon EC2 m4.xlarge ... [Read more...]

A little while ago I demonstrated how to extract FASTQ from MinION FAST5 files using Rscript and the Linux command line. In that article, I described how to extract the different FASTQ data using a parameter: # 2D is the default invisible(apply(array(f5files), 1, printfastq)) # template invisible(apply(array(... [Read more...]