I'm not completly sure if I fully understand the question.
But the 4th input for the scatter command can be used to indicate the collor.
See the example code below, hope it helps:
n = 200;
dat1 = rand(n,1);
dat2 = rand(n,1)*0.50;
dat3 = -rand(n,1)*0.25;
x_data = repmat((1:n)',3,1); % assume some x-data
y_data = [dat1;dat2;dat3]; % gather the y-data
c_data = repelem([1;2;3],n); % generate the color indices
figure
scatter(x_data,y_data,[],c_data,'filled')
grid on
