setMTEXpref('xAxisDirection','east');setMTEXpref('zAxisDirection','intoPlane');
Look at the image below. In the import wizard there is an option to rotate the data. At the end of the script generated by the import wizard you will find these lines:
%% Correct Data
rot = rotation('Euler',90*degree,90*degree,0*degree);
ebsd1 = rotate(ebsd1,rot);
That is the command to rotate the data. If you use the import wizard it will appear automatically.
This example is the importation of EBSD data, but if you are importing PF data you will find something similar in the import wizard.
The angles you have to rotate will depend on how you acquired the data.