Comments (2)
Not easily. It is far easier to recreate the ordination with vegan functions and then plot with gg_ordipolot:
library(ade4)
library(vegan)
library(ggordiplots)
sam <- MiDASsubset$metadata
otu <- t(MiDASsubset$abund)
otu.hel <- decostand(otu, "hellinger") # By default, amp_ordinate makes this transformation.
d <- vegdist(otu.hel, "bray")
add <- !(is.euclid(d)) # Corrects for negative eigenvalues if necessary
pcoa <- cmdscale(d, k = nrow(otu)-1, eig = TRUE, add = add)
plt <- gg_ordiplot(pcoa, groups = sam$Plant, plot = FALSE)$plot
plt + theme_minimal() + labs(color = "Plant")
I did notice that the percent variation associated with the axes in your plot are incorrect.
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Thanks so much! I think I'll do it this way... I'm not so sure abt the percent variation though. Maybe it could be due to the Hellinger transformation.
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