You can run a MATLAB file that does not produce a visual output in the MATLAB analysis app. For visualization outputs, use the MATLAB Visualizations app. Both of these are available on ThingSpeak under the apps menu after you log in.
There are certain functions that are not allowed, for example UI elements. There are a limited number of toolboxes that are supported, you must use the same MathWorks account that you are licensed to use toolboxes in ThingSpeak.
Please let us know if you have trouble running your files.