PeerJ, like PLoS ONE, aims to publish work on the basis of “soundness” (scientific and methodological) as opposed to subjective notions of impact, interest or significance. I’d argue that effective, appropriate data visualisation is a good measure of methodology. I’d also argue that on that basis, Evolution of a research field – a micro (RNA) example fails the soundness test.
6-way Venn banana
I thought nothing could top the classic “6-way Venn banana
“, featured in The banana (Musa acuminata) genome and the evolution of monocotyledonous plants
That is until I saw Figure 3 from Compact genome of the Antarctic midge is likely an adaptation to an extreme environment.
5-way Venn roadkill
What’s odd is that Figure 2 in the latter paper is a nice, clear R/ggplot2 creation, using facet_grid(), so someone knew what they were doing.
That aside, the Antarctic midge paper is an interesting read; go check it out.
This led to some amusing Twitter discussion which pointed me to *A New Rose : The First Simple Symmetric 11-Venn Diagram.
[*] +1 for referencing The Damned, if indeed that was the intention.
A recent question over at BioStar asked whether abstracts returned from a PubMed search could easily be visualised as “word clouds”, using Wordle.
This got me thinking about ways to solve the problem using R. Here’s my first attempt, which demonstrates some functions from the RCurl and XML packages.
update: corrected a couple of copy/paste errors in the code
Read the rest…
The Life Scientists 2009
It’s Christmas Eve tomorrow and so I declare the year over. My Christmas gift to you is a summary of activity in 2009 at the FriendFeed Life Scientists group
. It’s crafted using R + Ruby, with raw data and some code snippets available. If you want to see the most popular items from the group this year, head down to the bottom of this post.
(Note: this post is a work in progress)
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Here’s a common problem solved: how to generate a pretty picture of your database schema. A Google search throws up all manner of home-brewed solutions using graphviz, perl scripts and so on. Or you can make life easier and simply install SQLFairy
Under Ubuntu: as simple as “sudo apt-get install sqlfairy”.
Next, dump your database tables, e.g. for MySQL:
mysqldump -u username -p -d mydatabase > mydatabase.sql
Finally, for a PNG image of your schema:
sqlt-graph -f MySQL -o mydatabase.png -t png mydatabase.sql
Too easy. Example shown is the BioSQL schema.
update: if your schema lacks explicit foreign keys, try the –natural-join options (man sqlt-graph, man sqlt-diagram)
Twitter Friends FOAF view
I’m liking TwitterFriends
I agree. Finally, social network visualisation that tells you something useful; e.g. well-connected people = useful to know. All without asking for your password too.
Would it tell us anything useful? Does it tell us anything useful about the current state of journal RSS feeds, or suggest areas for improvement?
Let’s find out. It’s as simple as locating the feed URL from your journal subscriptions, pasting it into Wordle and eyeballing the results. Here’s what came back for the 25 journals in my current subscription list.
Read the rest…