My favourite graphing and plotting software

Preparing graphics for experimental write-ups is always a bit of a minefield. Everyone has their favourite software for preparing histograms, plots and charts and if you’re happy with a program and have a good handle on how it works, you’re probably best off sticking with what you know. For me though, the important aspects when choosing a bit of software to use in this area are primarily aesthetic – I like very clean-looking, uncluttered charts which maximise clarity and readability. Before talking about my favourite bits of software I’ll talk about one that you definitely should not use – Microsoft Excel.

A ‘classic’ MS excel chart. Fugly. Avoid.

Excel is great for a lot of things, but making plots is not one of them. The older versions of Excel in particular just look awful, yet I still see these kinds of plots in so many published papers – every time I see one I do a massive internal facepalm; it just looks totally amateur-ish. The newer versions look a bit better, but still – to be avoided if you want to be taken seriously. Also, for the love of God, never use anything like this:

Excel 3D chart. This way doth madness lie.

3D-effect histograms do not make your data look cool and professional. They are for shiny-suited advertising executives and madmen. End of discussion.

So, what should you use? For years, I was a big fan of SigmaPlot; a very powerful program with a whole host of awesome features that produces some really beautiful results. Unfortunately, I never found the user interface very friendly or intuitive – for most users there’s a fairly steep learning curve involved in using it, but it does produce really nice results, so it’s worth persevering. The level of customisation and formatting options available for your plots are fantastic, and well beyond anything you can achieve in Excel. One other great feature is that SigmaPlot will export plots as very high-quality bitmaps or tiffs (up to 600dpi) for incorporation into figures for papers.

SigmaPlot screenshot with a very pretty plot.

I stuck with SigmaPlot for years because I liked the results, and I (eventually) got comfortable with the interface. However, since switching to (mostly) using a Mac a couple of years ago, I’ve been searching for a good replacement (SigmaPlot is unfortunately PC-only). I think I’ve finally found one – GraphPad Prism. Prism produces really nice, high-quality, simple-looking plots, plus the interface is mercifully friendly, with a lot of built-in demos using sample data which you can modify with your own data very easily.

A sample Prism plot – simple, clear, clean… nice.

The unfortunate downside of both SigmaPlot and Graphpad Prism is that they are both commercial pieces of software which cost real money (although Prism does have a 30-day trial period in which you can try it out). I normally like to recommend free software on this site, but unfortunately I’ve never found anything which compares to these two recommendations in the freeware/shareware world. People have told me that R can produce some very nice plots, and I’m sure they’re right, but because of the command-line interface it’s something that I’d hesitate to recommend for beginners/students. I’ve also had a good poke-around online and haven’t found any decent online tools for making nice-looking basic plots. Well, there’s this one, which (bizarrely) seems to be aimed at kids, and this one which seems OK-ish (but requires sign-up, so y’know… fail) but they’re nothing I’d heartily recommend.

If anyone has any other suggestions for their favourite (preferably free!) software for this kind of thing, whether online or offline, please let me know in the comments! Happy plotting!

TTFN.