The Quality of Scientific Plotting Software

I’m going to take a minute here to rant a little bit about the paltry menu of scientific plotting software that is available.

This research project that I’m working on has required me to teach myself the basics of multivariate linear regressions and a few other things. I’ve finally gotten something that I think is legitimate, although I won’t know until tomorrow, when I meet with the physician I’ve been working with. I want to make some simple box-and-whisker plots that show the differences between a few different groups. I’ve been using JMP to do my analysis, but I’d like to produce some publication quality figures so that I can start working on our paper. The problem is that the options for generating publication quality figures absolutely sucks. I’ve spent the past six hours trying to figure out the best way to generate a half dozen plots that don’t look like they were cobbled together in Excel and I’ve gotten nowhere. Screw all of this.

This isn’t the first time I’ve had this type of frustration. Here are the options I’ve tried, that produce crappy results.

• Matlab is nice for working with large datasets, particularly if you’re doing things like Fourier analysis or numerical modeling.  The problem that Matlab has is that it can’t produce reliable figures – what you see on your screen is usually not what you get when you generate an EPS or TIF.  Also, what the hell is with medical journals that don’t want vector images?  I was blown away when I found out that the journal I’m hoping to submit wanted GIF or JPG figures.  At any rate, Matlab is terrible.
• JMP is fine for producing quick plots of various statistical relationships, but its ‘Graph Builder’ is absolutely useless.  Beyond useless.  Honestly, the vast majority of statistical software I’ve used has the most worthless user interface.  It’s enough to make me think that GUI statistical software can shove it.  If I get into a MD / PhD program, I swear I will never use any of this crap – I’ll teach myself to use R and never look back.
• SigmaPlot.  This piece of crap costs a zillion dollars and the interface is nearly impossible to use.  It’s as if these packages are designed by people that don’t actually know anything about how data analysis is done.
• Microsoft Excel.  I hate almost everything Microsoft does, but Excel 2003 was awesome.  Of course, after that, Microsoft changed the interface entirely that is completely useless and makes the simplest tasks a Herculean epic.  Of course, there’s the problem of no capacity to export into a usable format.  Worthless

Seriously.  This is infuriating.  It should not be this difficult to produce properly formatted and sized figures.  Even the most expensive programs do an abysmal job.  All I want to do is make a few box-and-whisker plots with well-defined resolutions, fonts, formats, and sizes.  I have wasted countless hours trying to do this and I’m absolutely fed up with it.  Seriously, fuck this.