I have some issues with plotting the associations- the features pdf plots created are empty. The heatmap.pdf are OK, but the .pdf is always empty. There is no error or warning on the log file bur it seems that it tries to plot only the first feature in the first metadata and then stops…
Did anyone came across with that issue? have any idea how to solve it?
I can of course plot it by myself, is there a way to save the transformed and normalized feature table while running maaslin?