The figures created by App Designer are based around web technologies (like HTML and CSS) while the separate figures are based around Java technologies. Because of the different implementations, it is not unexpected that you may see some performance differences. However, the specific details depend a lot of the specifics of what you are plotting.
Can you provide more details about your app and what you are plotting? If not the actual data and code:
- What release of MATLAB are you using? The specific version of MATLAB can be important in diagnosing performance issues.
- What types of objects or graphics commands are you using?
- Roughly how many data points are you using?
- Do you know roughly how many graphics objects are you creating?
- Have you tried profiling your code to see what is taking the longest?