Wednesday, August 27, 2008

I love making figures! I hate making figures!

I am deep in figure making and paper writing at the moment, which is why blogging, and the science book list, are languishing. But figure making is obviously is a good thing, and a much better place to be than, say, having no data to make figures. Still though, it's a difficult process for me, probably because I'm an anal retentive freak about figures, but also it's a challenging intellectual and creative act.

Figure 1: Nat's inspiration for figure making. (damn Phil Hartman was one funny dude)."This one's a little bigger than the rest, so we'll just discard that one. [pulls out another piece] And I don't think this little wrinkly one belongs in here. [pulls out another] And this ... well, I just don't like the look of that one at all. Alright, as a matter of fact, why don't we just start over and throw this out? [places bowl on counter]"

Good things about making figures:

As said above, it means you have data.

After 11 years of using Igor for data analysis and figure presentation, there are very few annoying questions like, "I want these symbols to stand off the x-axis, how do I do it?" Or, "why is there a limit in the number of columns I can have?" And since all my initial analysis there as well, there's no added importing data, etc.

It's rewarding to make something. Figure making is something where you can really bring out your creativity and where you can distinguish yourself. There's just something satisfying about seeing that figure, which distills the essence of your experiments, come together.

Bad things about making figures:

It hurts. Literally. Maybe my computer/desk set up isn't a paragon of ergonomic-osity, but it isn't so bad. Still, gimme a few days of dragging labels around to get them where I want them (as I said, anal retentive, see Fig. 1) brings out the repetitive stress injury like kegs of Busch bring out the new freshmen (who by the way, are descending upon Boston like locusts. What hell, I thought it wasn't much of a college town?).

It hurts. Like in the brain. The process of defining exactly what you want to convey in every figure panel, and then realizing that on paper is hard. For me it's a relentlessly iterative process, starting out with an idea in my mind's eye, which then undergoes radical alterations (Fig.1). Sure, this is what it's all about, but that doesn't make it easy. Ask an artist. You think their process is easy?

Sometimes it's hard to find all the appropriate expts for a given point you want to make. This is just partly my own organization problem, but sometimes I really wish you could easily add tags to your data files, and then use those for searching. But, prior to the arrival of offspring, this wasn't as much of an issue, since it fit pretty well up in my noggin, but a good couple of years of crap sleep has wrecked my memory. So now I need to keep much more explicit records for this. Which I'm getting much better at, but unfortunately doesn't apply retroactively.

Sometimes you realize you wish you had done certain experiments a little differently. Not so much that what you're thinking was wrong, but sometimes things like exact timing of solutions or voltage steps could be a little different, or some cells were recorded a little differently than others. This just makes talking about the figure painful. (Again, see Fig. 1).

The toner! The paper! I think I've printed 20 versions of this current figure I'm working on, and it's not even done. Well, what's a rich lab good for if not for profligate supply usage?

Ok, time to get back to the figures! I am interested to hear about others' figure making thoughts and feelings.


Erik said...

What hell, I thought it wasn't much of a college town?

Nice! Can't slip that passed me...

Drugmonkey said...

learn to mouse with your off-hand, it is easier than you think.

Dr. Jekyll and Mrs. Hyde said...

Hey, can you elaborate on tagging good figure-ready data as you get it? Do you keep a running list of Poifekt Cellz or what?

Nat Blair said...

@Erik - all is right with the universe

@DM - You'd think that switching to my left hand, that being my dominant in nearly all things but somehow not mousing, would be easy-peasy. And it does help, with anything but fine movements. I prefer to use the command line and keyboard shortcuts for as many things as possible. Yet somehow, dragging tiny little letters around to label current traces isn't one of them.

@DrJ&MrsH - Well, the tagging scheme I have in mind isn't really implemented. That would likely be an OS level thing, where you could add tags anywhere (in the program creating the data, or analyzing the data, or in window displaying the file info) and then easily search those tags via OS or other programs.

But I do try and highlight those cells which are likely to be decent as I record/analyze them. I still have a big old Excel file that shows all my recordings and any important notes about them (cell conditions, internal, etc) and I asterisk or fill the fields with a given color to show it's a good on.

The problem with that is that the file is still mostly manually input, which is ok, but could be made easier. I'm brainstorming ways of automating it (mostly through text files, which are easy to read and write via Igor).

How easy it is tag a cell as possibly figure worthy really depends on what "phase" i am in the project. Early pilot stuff, or later, "get a few more n, I have the right conditions figured out now" period. Hard to know exactly what you're looking for in the first, but it's usually pretty obvious in the latter.