I have a dataset consisting of ~1500 female samples and ~1600 male samples, both with the exact same variables and similar distributions between the two sexes. I've stratified this dataset based on sex and made a separate UMAP for them both. I then attempted to project the male dataset into the female UMAP space and vice versa using umap_transform, which worked fine for the female samples, and worked fine for most of the male samples, except that about 100 male samples got projected onto a ring surrounding the other datapoints, far away from them. I then reduced my male dataset to be the same size as the female dataset by removing the last 100 samples (the order of the samples is completely random) and this ring disappeared.

newCoor_female <- umap_transform(strat_dat$Female[,-1], umap_res$Male)
newCoor_male <- umap_transform(strat_dat$Male[1:nrow(strat_dat$Female),-1], umap_res$Female)

umap_res_gb <- umap_res
umap_res_gb$Female$embedding <- newCoor_female
umap_res_gb$Male$embedding <- newCoor_male


umap_res_gb %>%
  map(pluck, "embedding") %>%
  map(data.frame) %>%
  bind_rows(.id = "sex") %>%
  ggplot(aes(X1, X2)) +
  geom_point(alpha = .5, size = 1) +
  facet_wrap(~sex, nrow = 1, scales = "free") +
  theme_bw() +
  labs(x = "UMAP1", y = "UMAP2")

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