Publications by nsaunders
Nice graphic? Are they taking the p…
Yes, it started with a tweet: Nice graphic on urine components via https://t.co/sfuXNB02sF pic.twitter.com/vhVLahQ8su — Metabolomics (@metabolomics) January 31, 2017 By what measure is this a “nice graphic”? First, the JPEG itself is low-quality. Second, it contains spelling and numerical errors (more on that later). And third…do I have...
2739 sym R (1100 sym/3 pcs) 8 img
Hyetographs, hydrographs and highcharter
Dual y-axes: yes or no? What about if one of them is also reversed, i.e. values increase from the top of the chart to the bottom? Judging by this StackOverflow question, hydrologists are fond of both of these things. It asks whether ggplot2 can be used to generate a “rainfall hyetograph and streamflow hydrograph”, which looks like this: My f...
2005 sym R (1272 sym/2 pcs) 10 img
Twitter Coverage of the Lorne Genome Conference 2017
Things to know about Lorne in the state of Victoria, Australia. It’s situated on the Great Ocean Road, a major visitor attraction and a great way to see the scenic coastline of the region It’s home to a number of life science conferences including Lorne Genome 2017 This week’s project then: use R to analyse coverage of the 2017 meeting on...
1662 sym 6 img
HTML vignettes crashing your RStudio? This may be the reason
Short version: if RStudio on Windows 7 crashes when viewing vignettes in HTML format, it may be because those packages specify knitr::rmarkdown as the vignette engine, instead of knitr::knitr and you’re using rmarkdown v1. Longer version with details – read on. update: looks like this issue relates to the installed version of rmarkdown (1.3 ...
1964 sym R (309 sym/1 pcs) 8 img
The nhmrcData package: NHMRC funding outcomes data made tidy
Do you like R? Information about Australian biomedical research funding outcomes? Tidy data? If the answers to those questions are “yes”, then you may also like nhmrcData, a collection of datasets derived from funding statistics provided by the Australian National Health & Medical Research Council. It’s also my first R package (more correct...
5179 sym R (141 sym/1 pcs) 12 img
An update to the nhmrcData R package
Just pushed an updated version of my nhmrcData R package to Github. A quick summary of the changes: In response to feedback, added the packages required for vignette building as dependencies (Imports) – commit Added 8 new datasets with funding outcomes by gender for 2003 – 2013, created from a spreadsheet that I missed first time around – ...
1111 sym 6 img
Visualising Twitter coverage of recent bioinformatics conferences
Back in February, I wrote some R code to analyse tweets covering the 2017 Lorne Genome conference. It worked pretty well. So I reused the code for two recent bioinformatics meetings held in Sydney: the Sydney Bioinformatics Research Symposium and the VIZBI 2017 meeting. So without further ado, here are the reports in markdown format, which displa...
1054 sym 6 img
Chart golf: the “demographic tsunami”
“‘Demographic tsunami’ will keep Sydney, Melbourne property prices high” screams the headline. While the census showed Australia overall is aging, there’s been a noticeable lift in the number of people aged between 25 to 32. As the accompanying graph shows… Whoa, that is one ugly chart. First thought: let’s not be too hard on Fairf...
4553 sym 14 img
Hacking Highcharter: observations per group in boxplots
Highcharts has long been a favourite visualisation library of mine, and I’ve written before about Highcharter, my preferred way to use Highcharts in R. Highcharter has a nice simple function, hcboxplot(), to generate boxplots. I recently generated some for a project at work and was asked: can we see how many observations make up the distributio...
2267 sym R (943 sym/5 pcs) 8 img
Twitter Coverage of the Bioinformatics Open Source Conference 2017
July 21-22 saw the 18th incarnation of the Bioinformatics Open Source Conference, which generally precedes the ISMB meeting. I had the great pleasure of attending BOSC way back in 2003 and delivering a short presentation on Bioperl. I knew almost nothing in those days, but everyone was very kind and appreciative. My trusty R code for Twitter conf...
1144 sym 6 img