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What I want to do is very simple, I just cannot seem to get MATLAB to do it. I would like to plot contours using my 2D data set.

My data set is large; 2 x 844240. I can do a scatter plot just fine,

scatter(Data(1,:), Data(2,:));

Reading through the forums I found Scatter plot with density in Matlab, where a hisogram was plotted. This would suffice, however, I would like to overlay the plots.

enter image description here

The issue is that they have different axis, my scatter data has an axis of [0 0.01 0 2500]; whereas the histogram is [0 100 0 100].

Is there a way to change the axis values of the histogram without modifying the image?

Thanks!

Community
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Bob Dole
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    From the question, it's not very clear what you would be contouring. To get to contours, there needs to be a value in the 3rd dimension. It sounds like you might be trying to plot the point density, is that correct? – TTT Nov 19 '14 at 19:57
  • Yes you are correct, although, a contour plot of the point density would be great (which I can do from the below answer). Thank you for your comment, always appreciated! – Bob Dole Nov 20 '14 at 14:15

1 Answers1

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If I understand correctly, you are using hist3 to construct a histogram and then using imagesc to plot it. You can use the second output argument of hist3 to get the histogram bin centers, and then pass those on to imagesc, e.g.

nBins_x = 100;
nBins_y = 100;
[counts, bin_centers] = hist3(Data, [nBins_x nBins_y]);
x_bin_centers = bin_centers{1};
y_bin_centers = bin_centers{2};
imagesc(x_bin_centers, y_bin_centers, counts)

A couple other notes:

  • In your case, you will need to transpose your [2 x N] matrix when passing it to hist3, which expects an [N x 2] matrix.

  • imagesc puts the first axis (which I've been calling the "x" axis) on the vertical axis and the second on the horizontal axis. If you want to flip it, you can use:

    imagesc(y_bin_centers, x_bin_centers, counts')

  • If you want to specify the histogram bins explicitly (e.g. to match your scatterplot) you can specify that in the arguments to hist3:

    x_bin_centers = linspace(0, .01, 100);
y_bin_centers = linspace(0, 2500, 100);
counts = hist3(Data, {x_bin_centers, y_bin_centers};

And if you want a contour plot, you can use (note that contour takes the axes arguments in a different order than imagesc):

contour(x_bin_centers, y_bin_centers, counts');

If you are unhappy with the jaggedness of the contours, you may consider using a kernel density estimate instead of a histogram (check out ksdensity) (oops, looks like ksdensity is 1-D only. But there are File Exchange submissions for bivariate kernel density estimation).

KQS
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  • This sounds like it would work! I will give it a try later today! Thanks, I really appreciate the amount of detail in your response. – Bob Dole Nov 19 '14 at 21:08
  • Upon trying your code, I find that the axis in the figure do not change with the plot. Therefore, I am left with a line (since the x data is only from 0 to 0.01, but the x-axis is showing from 0 to 100). I think everything is plotting correctly, I just need a way to display it properly. Do you have any suggestions? I have tried using `set(gca,'xlim',[0 0.01]);` with no avail. – Bob Dole Nov 20 '14 at 14:12
  • Sorry, my mistake. I had `axis equal` which messed it up. Thanks again! Worked like a charm! – Bob Dole Nov 20 '14 at 14:49