Some Matlab tricks for making figures 
[Sep. 17th, 200707:50 pm]
Tobin Fricke's Lab Notebook

When generating figures for publication from within Matlab, one annoyance (of many!) is the unnecessary whitespace that Matlab introduces. One would prefer Matlab to make the bounding box as tight as possible and let LaTeX handle the whitespace.
It turns out that an "axes" in Matlab has three properties which determine its positioning: OuterPosition, Position, and TightInset. OuterPosition gives the coordinates of the entire region within the current figure belonging to the axes. Position gives the region contained by the "data" region of the axes. TightInset gives the distance beyond this "data" region which is used by tick marks, labels, titles, and other decorations. Here's a sample plot with the OuterPosition illustrated in yellow, the Position in magenta, and the TightInset in red:
Notice the space between the red rectangle and the boundary of the image. Why is that there? We can eliminate it by setting Position to be equal to OuterPosition minus the margins given by TightInset:
set(gca, 'Position', get(gca, 'OuterPosition')  ... get(gca, 'TightInset') * [1 0 1 0; 0 1 0 1; 0 0 1 0; 0 0 0 1]);
That little matrix is there because OuterPosition and Position are stored as [x_0 y_0 width height] whereas TightInset is [dx_left dy_bottom dx_right dy_top] . The results are:
Voilà! The offending whitespace has been removed. (For some reason, however, Matlab, seeing your modification of Position, takes it upon itself to compute a new, nonsensical value of OutsidePosition. This seems to be harmless...)
Another annoyance is in getting your figure to be the right size. Sure, you can scale your figure, but then the fonts will be the wrong size. The easiest thing to do is to estimate the desired size of your final figure, and have Matlab generate the figure in the correct size to begin with. The trick is to force not just the PaperSize but also the PaperPosition. If we want a figure 6.25 inches by 7.5 inches, we would do this:
set(gcf, 'PaperUnits', 'inches'); set(gcf, 'PaperSize', [6.25 7.5]); set(gcf, 'PaperPositionMode', 'manual'); set(gcf, 'PaperPosition', [0 0 6.25 7.5]);
A yet further annoying situation is this: you dutifully utilize PDF or EPS files for your figures, and yet they appear to be included as ugly, nonscalable raster graphics! I encountered this problem just today. Matlab allows you to choose between several renderers, which determine just how your figures get made. Suppose you have utilized transparency in your figure, yet are asking Matlab to output a figure to PDF, which (in the version supported by Matlab) does not support transparency. What's Matlab to do? Here's what it does do: it takes a screenshot, producing a bitmap, which is then wrapped in EPS or PDF. Doh!
The trick is to ask Matlab to use the "painters" renderer. It does not support transparency, but at least you're guaranteed vector graphics output:
set(gcf, 'renderer', 'painters');
Finally, just for the sake of completeness, you might want to actually generate your output file:
print(gcf, 'dpdf', 'myfigure.pdf'); print(gcf, 'dpng', 'myfigure.png'); print(gcf, 'depsc2', 'myfigure.eps'); 

