Blog Archives

Years as coloured bars

August 5, 2017
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Years as coloured bars

I keep seeing years represented by coloured bars. First it was that demographic tsunami chart. Then there are examples like the one on the right, which came up in a web search today. I even saw one (whispers) at work today. I get what they are trying to do – illustrate trends within categories over … Continue reading Years...

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Twitter Coverage of the ISMB/ECCB Conference 2017

August 2, 2017
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Twitter Coverage of the ISMB/ECCB Conference 2017

ISMB (Intelligent Systems for Molecular Biology – which sounds rather old-fashioned now, doesn’t it?) is the largest conference for bioinformatics and computational biology. It is held annually and, when in Europe, jointly with the European Conference on Computational Biology (ECCB). I’ve had the good fortune to attend twice: in Brisbane 2003 (very enjoyable early in … Continue reading Twitter...

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Twitter Coverage of the Bioinformatics Open Source Conference 2017

July 25, 2017
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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 … Continue reading Twitter...

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Hacking Highcharter: observations per group in boxplots

July 24, 2017
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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 … Continue reading Hacking...

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Chart golf: the “demographic tsunami”

July 20, 2017
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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 Fairfax … Continue reading Chart...

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Visualising Twitter coverage of recent bioinformatics conferences

June 20, 2017
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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, … Continue reading Visualising...

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An update to the nhmrcData R package

March 15, 2017
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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 … Continue reading An...

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The nhmrcData package: NHMRC funding outcomes data made tidy

March 8, 2017
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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 correctly, R data … Continue reading The...

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HTML vignettes crashing your RStudio? This may be the reason

March 5, 2017
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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 in my … Continue reading HTML...

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Twitter Coverage of the Lorne Genome Conference 2017

February 16, 2017
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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 … Continue reading Twitter...

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