I have two sections of code (each section starts with %%), they both have plots in them. When I go to publish, the first section shows the plot immediately after the section/block of code it corresponds to, but the second section doesn't produce the plot. It has something to do with the last section. I repeated the second block of code, so there were a total of 3 sections and the first two sections had plots after them but the last did not. When I run the script both/all plots are produced with no errors. In other words both code blocks are producing the right plots. It's just when I publish for some reason the last section doesn't produce a plot. I don't want to use snapnow because that puts the plots at the very end of the script and I want them to show up after their corresponding code.
Note: there is a section with a function at the very end – could this be affecting it?