Q: text in PDF figures disappear in journal submission systems When processed with pdflatex, my PDF figures work charm. However, when I uploaded the PDF document to some journal submission systems, some texts in the PDF figures disappear in the preview document that is processed by the journal submission system.
I do not understand how exactly the journal submission systems process the PDF manuscript files, but how can I prevent such problems from occuring? Is there any special way to compile the tex file, or any special way of preparing the PDF figures? Some are saved in MATLAB as PDF, and some are saved in Powerpoint as PDF.
The particular journal submission systems are those by Scholar One at http://mc.manuscriptcentral.com/XXXXX.

A: One possibility is that the PDF has been made without embedding (and subsetting) the fonts, which is often required by journals. 
To check, at least on a linux machine, you can use:
[romano:~/education … Bio/Quizzes/Q2] % pdffonts t2-1.pdf
name                                 type              encoding         emb sub uni object ID
------------------------------------ ----------------- ---------------- --- --- --- ---------
EEFOFU+Symbol                        Type 1C           Custom           yes yes no       8  0
UYAERB+Times-Roman                   Type 1C           WinAnsi          yes yes no      10  0

in this case all fonts have been embedded and subset (see the emb and sub column). 
More info on how to obtain the result in How to embed fonts at compile time with pdflatex and in the documentation of IEEE testflow package. 

A: I had the same problem, where figures were generated only with R. The solution was to use the function embedFonts from R package grDevices on the final manuscript pdf (produced by pdflatex).

library(grDevices)
embedFonts("manuscript.pdf", outfile="manuscript_withfonts.pdf")

