You could arrange a custom track in the UCSC Genome Browser with your signals of interest, over your genomic region of interest, and then export a screenshot to PDF.
The custom track would contain your 5-hmC and 5-mC signals (or whatever other signal you are visualizing). These could be bigWig files, for instance, which contain your signals of interest.
Once you have loaded your custom track, append a gene annotation track (refGene, Gencode, etc.).
Follow the instructions to export a PDF screenshot. You can edit this PDF with Adobe Illustrator to make a publication-quality figure.
How can I take a screen shot of a Genome Browser track display for publication?
To print or save a Genome Browser tracks image to a file, click the
"PDF/PS" link from the "View" menu of the blue navigation bar at the
top of the tracks page, then choose your preferred format. This will
save a copy of the currently displayed annotation tracks image to a
file that can be printed or edited. Images saved in PostScript format
can be printed at high resolution and edited by drawing programs such
as Adobe Illustrator. This is particularly useful for generating
figures intended for publication. Images saved in PDF format may be
viewed by Adobe Acrobat Reader.
This is useful for generating a one-off figure.
If you have two or more regions for which you want to see the same signal tracks, and you want to automate or script this process, you could use the UCSC Genome Browser in conjunction with a command-line tool like soda.py.