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

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 ?