MATLAB - Pixelize a plot and make it into a heatmap

I have a matrix with x and y coordinates as well as the temperature values for each of my data points. When I plot this in a scatter plot, some of the data points will obscure others and therefore, the plot will not give a true representation of how the temperature varies in my data set.

To fix this, I would like to decrease the resolution of my graph and create pixels which represent the average temperature for all data points within the area of the pixel. Another way to think about the problem that I need to put a grid over the current plot and average the values within each segment of the grid.

I have found this thread - Generate a heatmap in MatPlotLib using a scatter data set - which shows how to use python to achieve the end result that I want. However, my current code is in MATLAB and even though I have tried different suggestions such as heatmap, contourf and imagesc, I can't get the result I want.


You can "reduce the resolution" of your data using accumarray, where you specify which output "bin" each point should go in and specify that you wish to take a mean over all points in that bin.

Some example data:

% make points that overlap a lot
n = 10000
% NOTE: your points do not need to be sorted.
% I only sorted so we can visually see if the code worked,
% see the below plot
Xs = sort(rand(n, 1));
Ys = rand(n, 1);
temps = sort(rand(n, 1));

% plot
scatter(Xs, Ys, 8, temps)

(I only sorted by Xs and temps in order to get the stripy pattern above so that we can visually verify if the "reduced resolution" worked)

Now, suppose I want to decrease the resolution of my data by getting just one point per 0.05 units in the X and Y direction, being the average of all points in that square (so since my X and Y go from 0 to 1, I'll get 20*20 points total).

% group into bins of 0.05
binsize = 0.05;

% create the bins
xbins = 0:binsize:1;
ybins = 0:binsize:1;

I use histc to work out which bin each X and Y is in (note - in this case since the bins are regular I could also do idxx = floor((Xs - xbins(1))/binsize) + 1)

% work out which bin each X and Y is in (idxx, idxy)
[nx, idxx] = histc(Xs, xbins);
[ny, idxy] = histc(Ys, ybins);

Then I use accumarray to do a mean of temps within each bin:

% calculate mean in each direction
out = accumarray([idxy idxx], temps', [], @mean);

(Note - this means that the point in temps(i) belongs to the "pixel" (of our output matrix) at row idxy(1) column idxx(1). I did [idxy idxx] as opposed to [idxx idxy] so that the resulting matrix has Y == rows and X == columns))

You can plot like this:

imagesc(xbins, ybins, out)
set(gca, 'YDir', 'normal') % flip Y axis back to normal

Or as a scatter plot like this (I plot each point in the midpoint of the 'pixel', and drew the original data points on too for comparison):

xx = xbins(1:(end - 1)) + binsize/2;
yy = ybins(1:(end - 1)) + binsize/2;
[xx, yy] = meshgrid(xx, yy);
scatter(Xs, Ys, 2, temps);
hold on;
scatter(xx(:), yy(:), 20, out(:));

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