Figures generated in RMarkdown when compiling to PDF have axes cut off

Is this the same issue as in these other ones ?

It is hard to follow with the 3 opened thread.

I answered in Different Rmarkdown to PDF compiler behavior with RMarkown and Bookdown - #2 by cderv

There is a cropping by default with PDF when some tools are present. The fig_crop = TRUE argument as always been there but conditionnal to some tool you may not had before maybe. See function help page

fig_crop
Whether to crop PDF figures with the command pdfcrop. This requires the tools pdfcrop and ghostscript to be installed. By default, fig_crop = TRUE if these two tools are available.

Only on Windows the default behavior may have change some time ago.

Can you set fig_crop = FALSE to see if this fixes it ?