scaling at two levels grouping in ggplot?

[marwa38]

I have three different phases (challenge, intermediate, and stimulus) and four different parts (distal, middle, and pyloric for the challenge; distal for the intermediate; whole for the stimulus) so I have two levels (treatment and part) which I need to appear in my ggplot The problem is that the distal appears in ggplot but doesn't mention if it is distal of intermediate or challenge, I think it merges both together.

ggplot(ps_phylum, aes(x = part, y=Abundance, color = Phlyum, group = Phylum)) +
stat_smooth(method = "loess") +
ylab("Relative Abundance") +
geom_point(size = 1.25, alpha = 0.4)

Could you please advise me on this? have tried facet_wrap and scaling funcitons without help.

[karawoo]

This type of question is a better fit for RStudio Community. I'd suggest asking there with a reproducible example. This issue tracker is intended for bug reports and feature requests.