If you have just two treatment categories then you can make two separate analysis for each level (selecting the data just for particular level). Just replace names Treatment1
and Treatment2
with actual names of your treatments.
kor1<-cor(Plants[Plants$Treat=="Treatment1",c(10:44)], use="pairwise.complete.obs", method="pearson")
kor2<-cor(Plants[Plants$Treat=="Treatment2",c(10:44)], use="pairwise.complete.obs", method="pearson")