I also recommend separating repetitive parts of plot generating code into template files, such as with mako or jinja2, and then programmatically generate sequences of plots by first piping the data into the jinja2 template, and then using insert commands to insert it into a bigger tex document.

I found this helpful when writing a paper where the appendix needed over 35 different tables of regression results, all with the same format but populated with data from different subpopulations, which would need to be regenerated (including updated captions, etc.) any time data cleaning or methodology was changed.