Welcome to the wonderous world of GUIs :)
You can label your figures. Normalized units can be changed to pixels, inches, centimeters etc. and you change the backmost numbers accordingly.
Then, when you plot something in your function, state which figure to update by calling the figure label. You can add as many figures into the same GUI as you want, and as long as you give them different "names", you can easily specify when to update what.
MYGUI=figure('toolbar','figure','MenuBar','none','Name','Sample GUI','NumberTitle','off','Color',[0.85 0.85 0.85],'Units', 'points','Position',[10 , 0, 1135 , 530 ]);
%This labels your GUI, and its name is now "MYGUI".
%That way, you define the figure "MyFigure" to belong to the "MYGUI" parent.
MyFigure = axes('Parent', MYGUI,'Units', 'normalized','HandleVisibility','callback','Position',[0.05,0.50,0.42,0.10]);
%And now, make a plot, add a legend, and label the y-axis on the figure you just labelled "MyFigure".
plot(MyFigure,x_data1,y_data1,'r-',x_data2,y_data2,'b-');
lgnd1=legend(MyFigure,'Sample data 1','Sample data 2','Location','SouthWest');
ylabel(MyFigure,'This label goes on "MyFigure"','FontSize',11,'Interpreter','latex');
