A little modified Jonas code to make background bars transparent and correct some errors:
%# define some parameters
foregroundColor = 'k';
backgroundColor = 'r';
foregroundWidth = 0.3;
backgroundWidth = 0.9;
%# collect the data
graph = [2 3 5 4 9 1 7];
color = [0 2 2 1 0 1 2];
x = 0:length(graph)-1;
colIdx = color>1;
bgBarHeight = max(graph)+1; %# background bars are 1 taller than max
%# first, plot foreground bars
b1 = bar(x,graph,foregroundWidth,'FaceColor',foregroundColor);
hold on
%# then, plot background bars.
%# they will overlap foreground bars, but we'll make them transparent later
b2 = bar(x,colIdx*bgBarHeight,backgroundWidth,'FaceColor',backgroundColor,'EdgeColor','none');
hold off
%# make background bars transparent
pch = get(b2,'child'); %# get patch objects from barseries object
set(pch,'FaceAlpha',0.3); %# set transparency
xlabel('X Axis')
ylabel('Y Axis')