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a) use subplot(2,3) and rearrange the two middle (make one invisible and move position of the second), or
b) draw them all individually where you want them.
Example for a) (which is what I think I'd do...)
h=zeros(6); for i=1:6, h(i)=subplot(2,3,i); end % make the six, save handles delete(h(2)) % wipe out the middle top one p=get(h(5),'position'); % position of middle bottom pt=get(h(1),'position'); % position of a upper p(2)=(pt(2)+p(2))/2; % center of bottom for the two rows set(h(5),'position',p) % move the middle to there... h(2)=; % remove the nonexistent handle
Just remember that they're numbered sequentially now in position as
1 3 1 2 5 --> 4 4 6 3 5
You can always rearrange the handles in the h vector--swapping h(3) and h(4) would put them from L to R, T to B which probably as easy an ordering as there is, consistent w/ subplot itself.
Here is a simple, general example of how to position two sets of axes in one figure.
ax1 = axes; ax2 = axes;
set(ax1,'Position',[0.5 0.5 0.35 0.25]) set(ax2,'Position',[0.1 0.1 0.25 0.35])
h1 = plot(ax1,rand(3,1),rand(3,1),'.'); h2 = plot(ax2,rand(3,1));
You can also adjust the size of the figure window itself with