"Is it possible to have both a in each group green; and have both b in each group yellow?"
Yes. Use the "colors" propery but include an extra color that will not appear to account for the gap which is actually a box plot of all NaN values that doesn't appear. Since you have 2 groups of 3 plots, set 4 different colors.
data = {rand(100,2), rand(20,2)*.8, rand(1000,2)*1.2};
boxplotGroup(data, 'Colors', lines(4)) % See image below
% Or
% data = {rand(100,2), rand(20,2)*.8, rand(1000,2)*1.2};
boxplotGroup(data, 'Colors', lines(4))
% or
boxplotGroup(data, 'Colors', 'rcmk') % string arrays also accepted
Alternatively, you can set the colors after creating the grouped box plot.
data = {rand(100,2), rand(20,2)*.8, rand(1000,2)*1.2};
h = boxplotGroup(data);
set(h.axis.Children(1).Children,'Color', 'r')
set(h.axis.Children(2).Children,'Color', 'k')
set(h.axis.Children(3).Children,'Color', 'g')
Image of first example
"is it possible to have 2 separate colors for these two groups that I have here?"
Not with this function. You might want to explore Matlab's boxplot function using the grouping variable and the ColorGroup property.
