This post assumes you’ve already figured out which variables to assign to which axes and found a good camera angle. I explain how to use AeroVis, a raster graphics editor, and a vector graphics editor to make a good-looking vector graphic that you can improve iteratively. It’s important to be able to do this because the first version of your figure will always need improvement: your glyphs were too small, or too large, or the wrong color. Or perhaps you need two similar figures: brushed and unbrushed, or the same glyphs with two different colorings. In any case, being able to make changes to your figures without starting from scratch will save you a lot of time.
Let’s take an example where you want to make two versions of a plot: one showing all of the glyphs, and another highlighting glyphs with a particular characteristic. You could do this purely in AeroVis, and it looks pretty good. But for really detailed control over the appearance of the figure, I recommend the procedure below.
Start in AeroVis with the view you like.
Camera View Settings
Before you go capturing any screenshots, carefully record the camera view settings. Do this by finding the camera settings icon on the view menu. Click it. It opens up the camera view settings dialog. Write everything down.
Double-check. Once you’ve captured the camera information, you can close AeroVis, come back later, and generate exactly the same image.
Capturing the Image
Open the Snapshot Controls dialog by clicking the snapshot icon in AeroVis.
Resize by a big factor. I like 5.0, but suit yourself and don’t be embarrassed to make a huge file.
Now turn off the axes and repeat. We’re going to make better-looking axes by hand, but we need to know where they are relative to the glyphs, which is why we made the first plot.
Creating the Vector Graphics File
Open up Illustrator or Inkscape. Make a layer called “reference.” Import the version of the image that has axes into your reference layer.
Now make a layer called “axes.” Using the reference layer as a guide, draw axes. You’re doing this because, while you can’t make the glyphs into smooth, beautiful vector graphics, you can fix the axes. Include whatever axes labels you want. I like to draw the back walls, but you could just do the principal axes, or the whole box like AeroVis does.
See how they aren’t all jagged like in the snapshot? That’s why we did this.
Open up the image that doesn’t have axes using a raster graphics editor like Photoshop or the Gimp. Add transparency to the current layer. Select the color white, and delete it. Now all that’s left is the glyphs and the legend. Note from Joe: This transparency idea is great. One benefit is you can draw things behind the glyphs if you’d like, such as gridlines. Also, you can use the “Lasso” tool to trace around the figure to remove previous labels, and if you use transparency to get rid of the whitespace, when you import it into another program, it will have nice and “clean” edges.
Over in your vector graphics editor, make a new layer. Call it “glyphs”. In Gimp/Photoshop, select the rectangle containing just the glyphs, then copy and paste it into the glyphs layer of your vector graphics image. Line up these glyphs with the glyphs in the reference layer, then hide the reference layer. Now you have a version of your glyph plot with nice axes!
Note from Joe: If you have problems copy/pasting like Matt suggests, you can save your copy/paste in a png (which preserves transparency) and turn compression completely off. I don’t think you use much quality doing this, and you have a copy of the file with no axes for your reference later on.
This is where it helps to have written down the camera settings. We’re going to make a second figure with certain glyphs emphasized. Go back to AeroVis, and enter your camera settings. Brush the data so that only your chosen glyphs are visible. Hide the axes, and take a snapshot.
Open the snapshot in your raster editor (Gimp / Photoshop). As before, add transparency, select and delete the color white. Make a new layer in your vector editor (Inkscape / Illustrator) above the axes layer but below the glyphs layer. Paste the glyphs there and line them up. You may need to hide the glyphs layer and use the reference layer instead, if you can’t see the ones you just pasted in. Adjust the transparency of the glyphs layer until there’s a clear distinction between your emphasized glyphs and your de-emphasized glyphs. The reason we put the new layer under the glyphs layer is that, with the transparency, it preserves the illusion of depth. Any glyphs that were obscuring the emphasized glyphs in the original screenshot still appear to be in front of the emphasized glyphs.