You could use this:
[ii, jj] = meshgrid(1:size(A,1), 1:size(A,2));
labels = strcat('(', num2str(ii(:)), ',' ,num2str(jj(:)), ')');
stem(reshape(A.',[],1)); %'// or plot, or bar, or...
set(gca, 'xtick', 1:numel(A))
set(gca, 'xticklabel', labels)
xlim([0, numel(A)+1])

To change color for each point: you can make use of hold all
:
[ii, jj] = meshgrid(1:size(A,1), 1:size(A,2));
labels = strcat('(', num2str(ii(:)), ',' ,num2str(jj(:)), ')');
hold all
B = A.';
for n = 1:numel(ii)
stem(n,B(n)); %'// or plot, or bar, or...
end
set(gca, 'xtick', 1:numel(A))
set(gca, 'xticklabel', labels)
xlim([0, numel(A)+1])

Or you could define a set of colors manually and use them consecutively within the loop:
[ii, jj] = meshgrid(1:size(A,1), 1:size(A,2));
labels = strcat('(', num2str(ii(:)), ',' ,num2str(jj(:)), ')');
colors = hsv(numel(A)); %// define colors
B = A.';
hold on
for n = 1:numel(ii)
stem(n,B(n), 'color', colors(n,:)); %'// or plot, or bar, or...
end
set(gca, 'xtick', 1:numel(A))
set(gca, 'xticklabel', labels)
xlim([0, numel(A)+1])
