I'm trying to find the best way to represent some microbiome data. First of all I've created a model using ZIBR so I can catch the abundance differences in my species regarding different condition. The "problem" that I have now is that I am trying to do a boxplot for different condition and as is an inflated by zero matrix, the boxplot is not very nice. What I've tried so far is to do a logit transformation over my abundance matrix (total sum is 100) as follow:

p <-ggplot(abundance_tmatrix, aes(x=Time_point, y=logit(abundance_matrix$ssp1) , color=treatment)) +
   geom_boxplot() + ggtitle("ssp1") +
   xlab("time") + ylab("logit(abundance)")

And it looks very nice, but I am not pretty sure if this is totally correct. Any advises? Thanks!