It seems like your function does the scatter plot. If it is possible to return the handle of the scatter plot as an output argument from the function, you could then use it to set the parent property of the scatter plot to the appropriate subplot axes. Alternatively you could also set the axes handle created using subplot and pass it to the scatter function as shown in the below link. This is useful to plot on the axes directly. <http://www.mathworks.com/help/matlab/ref/scatter.html#btrli6q-1 scatter >
The sample code below does subplotting of 2 scatter plots Using the handle from the scatter function, parent properties for the plots are set.
%x1 = -10:.1:10;
%y1=x1.^2;
%f1=figure('visible','off');
%h1=scatter(x1,y1);
%x2 = -5:.1:5;
%y2=x2.^3;
%f2=figure('visible','off');
%h2=scatter(x2,y2);
%figure
%a=subplot(1,2,1);
%b=subplot(1,2,2);
%set(h1,'parent',a);
%set(h2,'parent',b);
%close(f1,f2);
