Thank Kirill and Joe.
It seems that to create a separate html manual file is indeed the least painful, but the html file cannot include any iframe, otherwise, it can not be displayed in Shiny. So I have to write the manual in html, including a lot of math formulas. It's not easy to edit the file.
Using Google drive is another good way, it can even show the doc file in Shiny, however, the file must be set to public accessible. If the manual is confidential and private, this method doesn't work.
For some reason, tags$iframe(src="manual.pdf", width="900", height="600") doesn't work in my Shiny. I use Firefox.
I think frame and iframe functions need to be improved in Shiny.
Zhilan