Is it possible to presserve my animation and manipulation plots in the pdf?
You can export animations to SWF:
You can import them in LaTeX (see TeX SE):
(I had to insert the dimensions manually.)
Actually, *.avi or *. SWF can be read by Adobe Acrobat Pro.
You can try as Michael E2 did:
Use Adobe Acrobat Pro to open the file exported, i.e., C:\movie.avi.
Double click on the figure will animate it.