The problem is that axis positions are in figure space (relative to lower left corner of the figure) while the data point coordinates are in data space (relative to the origin). First you should convert your data point from data-space to figure space which will reqiure 1) knowing the data point's (x,y) coordinates, 2) knowing the x and y axis limits, 3) knowing the position of the axis in the figure.
% Example data
figure()
subplot(2,1,2)
C = [0 2 4 6; 8 10 12 14; 16 18 20 22];
imagesc(C)
hold on
plot(3,2,'kx','markersize',10)
% step 1: get data point's (x,y) coordinate
xyc = [3,2]; %already known
% step 2: get the x,y axis limits
hold on %we already did this but I included it again b/c it's important!
xl = xlim();
yl = ylim();
% setp 3: get axis position in figure
set(gca, 'Units', 'Normalize')
axpos = get(gca,'position');
% step 4: convert data coordinate from data space to figure space
xycNorm = (xyc - [xl(1),yl(1)])./[range(xl),range(yl)]; %normalized to axis
if strcmpi(get(gca, 'ydir'),'reverse')
xycNorm(2) = 1 - xycNorm(2); % This is needed iff y axis direction is reversed!
end
xycFigNorm = axpos(1:2) + axpos(3:4).*xycNorm; %normalized to figure
% step 5: create new axes
% If you want the axes to be centered on the coordinate, (SHOWN IN EXAMPLE BELOW)
axSize = [0.2, 0.2]; % size of new axes (normalized units)
ax2 = axes('Units','Normalize','Position',[xycFigNorm - axSize./2, axSize], 'color', 'none');
% If you want the new axes' lower-left corner to be aligned with the chosen coordinate
ax2 = axes('Units','Normalize','Position',[xycFigNorm, axSize], 'color', 'none')
