# Best way to display 3 variables with a scatter plot

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Flo on 8 Sep 2016
Commented: Walter Roberson on 13 Sep 2016
Hello everyone,
I am dealing with a small problem, and maybe some of you may have a better idea than me. So here is the story: I am having large datasets to display. By large I mean between 4K to 10K dots. I am using a scatter plot for that. I plot Y as a function of X and so far the results/display are ok. But I'd like to add the Z variable on the top of that.
My original idea was to display Z as a color variation. it goes from x.10-4 to ~5, and most of my values are very low: the result was few dots were yellowish and the rest was dark blue.
The second idea was to display the first, second and third quartile, with a color for each of them. I lose in resolution but I would have roughly my lower values in let's say blue, then red for 50% of my data, and finally the last 25% would be green. Here again the density of dots makes the graph difficult to read: the green is on the top of the red which is on the top of the blue....
Can I control the alpha with a scatter plot (as far as I've searched, I don't think so). Do you think of a better idea to display amount of dots in respects of the Z variable?
Here is my code :
temp = [X,Y,Z];
temp3= sortrows(temp,3);
N = length(X);
Q1= ceil(N/4);
Q3=ceil((3*N)/4);
a1=temp3(1:Q1,1);
b1=temp3(1:Q1,2);
c1=temp3(1:Q1,3);
a2 = temp3(Q1:Q3,1);
b2= temp3(Q1:Q3,2);
c2 = temp3(Q1:Q3,3);
a3=temp3(Q3:N,1);
b3=temp3(Q3:N,2);
c3=temp3(Q3:N,3);
figure();
scatter(a1(:),b1(:),10,c1(:), 'O', 'filled', 'b');
hold on;
scatter(a2(:),b2(:),10,c2(:), 'O', 'filled', 'r');
hold on;
scatter(a3(:),b3(:),10,c3(:), 'O', 'filled', 'g');
hold on;
axis( [0 1 1 5]);
Thank you for your help. Let me know if you need further information :)
Cheers, Flo
mbonus on 12 Sep 2016
To the best of my knowledge it's not a function in MATLAB but Excel does have it. For every x value you would find a percentage confidence value. This value is how much you can reasonably expect your data to deviate from the average with the confidence chosen. If you vectorize the calculation then you can plot it without a loop.
Walter Roberson on 13 Sep 2016
mbonus: sounds sort of like a box plot.

Walter Roberson on 13 Sep 2016
scatter() does not allow the alpha to be controlled on a per-point basis. It does, however, allow you to pass 'MarkerEdgeAlpha' and 'MarkerFaceAlpha' as scalars that affect all points drawn with that call.
Flo on 13 Sep 2016
I tried to play with those two parameters already, but they didn't permit me to access the dot properties.
Walter Roberson on 13 Sep 2016
Which MATLAB version are you using? And please explain what you mean about "access dot properties"