"Invalid Handle Object" when plotting 2 figures Matlab

Answer 1

When you call plot multiple times on the same figure, the previous plot is by default erased, and the handle to the previous plot points to nothing. Thus the error.

To fix this, you need to set the NextPlot property of the axes to add. You can do this by calling hold on (that's what you'd do if you were plotting from command line), or you can write

fig=figure;
%# create a set of axes where additional plots will be added on top of each other 
%# without erasing
axes('NextPlot','add');

If you want, you can store the axes handle as well, and use plot(ah,x,y,...) to make sure that you plot into the right set of axes and not somewhere strange if you happen to click on a different figure window between the time the figure is opened and the plot command is issued.