using Matlab to plot density contour for scatter plot

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Keqiao Li
Keqiao Li 2015-6-30
编辑： Walter Roberson 2023-2-8
Hi guys, I'm trying to use Matlab to plot the density contour for the following scatter plot. The bins will be 1X1 box. Within my limited understanding the density contour should be indicated how many points fall into the bins(correct me if I'm wrong), but I still cannot find a way to do the density plot. Need some help to solve this problem. Thanks!

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Mike Garrity
Mike Garrity 2015-6-30
Scatter doesn't do any binning. It's showing each individual data element.
Perhaps this approach does what you want?
x = randn(1,1000);
y = randn(1,1000);
n = hist3([x', y']);
pcolor(n)
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Keqiao Li
Keqiao Li 2015-7-2
Thank you Mike, I got what I want. Thank you for your help.
Andrea Ackroyd
Andrea Ackroyd 2018-12-3
I am commenting on this old post because I am doing a very similar thing, but achieving some unexpected results.
I am making a histogram2 (tile view) of one dataset, which is time samples of two variables. On the same axes I plot a contour of a map which comes from different data (essentially a target map for the time based data which is in the histogram).
The unusual behaviour is that the colour scale of the hist2 appears to be affected by having the contour on the same axes.
If it is noteworthy, I am plotting the contour first, with a solid colour for all contour lines (not using colormap). Then I plot the histogram second.

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Walter Roberson
Walter Roberson 2015-6-30
Assuming that your data starts at 0 and contains fractional values and is to be binned by 1 x 1, and that your coordinates are in X and Y,
xidx = 1 + floor(X(:));
maxxoff = max(xidx) - 1;
yidx = 1 + floor(Y(:));
maxyoff = max(yidx) - 1;
counts = accumarray([yidx, xidx], 1); %remember Y corresponds to rows
imagesc(counts, 'XData', 1/2+[0 maxxoff], 'YData', 1/2+[0 maxyoff]);
hold on
contour(1/2+(0:maxxoff), 1/2+(0:maxyoff), counts)
The 1/2 offsets have to do with referencing the centers of the boxes.
Elena De Angelis
Elena De Angelis 2016-1-14
编辑：Walter Roberson 2016-1-14
Hi, I'm trying to do the same but my result is not what I expect, could someone tell me please what i'm doing wrong?
x = dNBR_filt_CHANGE;
y = NBR_post_CHANGE;
scatter(x,y,'r.')
hold on
[n,c] = hist3([x, y]);
contour(c{1},c{2},n)
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geopap
geopap 2016-5-12
编辑：geopap 2016-5-12
I have exactly the same issue and unfortunately this doesn't work. Any other possible solution?
Update: In my case, where x and y are 1-column vectors, the n variable should be n'
Hamdullah OZOGUL
Hamdullah OZOGUL 2018-2-1
编辑：Hamdullah OZOGUL 2018-2-1
You just have to transpose the n to have the correct order.
contour(c{1},c{2},n')

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Jos? Manuel Amigo
Jos? Manuel Amigo 2017-11-11
编辑：Walter Roberson 2023-2-8
PCx = rand(2000,1); PCy = rand(2000,1);
bins = 50; Msize = 10;
[N C] = hist3([PCx,PCy],[bins bins]);
CX = C{1}; CY = C{2};
N2 = N; N2(N2 == 0) = []; Nunique = unique(N2);
colors = jet(length(Nunique));
for i = 1:length(PCx)
if isnan(PCx(i))
PCxnew(i,1) = NaN;
PCynew(i,1) = NaN;
J(i,1) = NaN;
else
whichoneX = find(min(abs(CX - PCx(i))) == abs(CX - PCx(i)));
PCxnew(i,1) = CX(whichoneX(1));
whichoneY = find(min(abs(CY - PCy(i))) == abs(CY - PCy(i)));
PCynew(i,1) = CY(whichoneY(1));
J(i,1) = sub2ind([bins,bins],whichoneX(1),whichoneY(1));
end
end
for i = 1:bins
for j = 1:bins
temp = sub2ind([bins,bins],i,j);
Jthese = find(J == temp);
if ~isempty(Jthese)
Ntemp = N(temp);
Nthis = find(Nunique == Ntemp);
plot(PCx(Jthese),PCy(Jthese),'.','color',colors(Nthis,:),'Markersize',Msize);
hold on;
end
end
end
hold off;

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