r - 相对丰度图的 Phyloseq 代码修改

Question

我正在关注这条管道（https://www.nicholas-olberding.com/post/introduction-to-the-statistical-analysis-of-microbiome-data-in-r/）以获取箱形图图像中的相对丰度，像这样（https://www.nicholas-ollberding.com/post/2019-07-28-introduction-to-the-statistical-analysis-of-microbiome-data-in-r_files/figure-html/box%20plot-1 .png）。

我尝试了以下代码

ps_phylum <- phyloseq::tax_glom(ps, "Phylum")
phyloseq::taxa_names(ps_phylum) <- phyloseq::tax_table(ps_phylum)[, "Phylum"]

phyloseq::psmelt(ps_phylum) %>%
ggplot(data = ., aes(x = Status, y = Abundance)) +
  geom_boxplot(outlier.shape  = NA) +
  geom_jitter(aes(color = OTU), height = 0, width = .2) +
  labs(x = "", y = "Abundance\n") +
  facet_wrap(~ OTU, scales = "free")

但我想修改像门级图这样的数字，但在这里，这些点将表示属/科/种。

Answer 1

我幸运地解决了这个问题，

ps_phylum <- phyloseq::tax_glom(ps, "class/order/family/genus")
phyloseq::taxa_names(ps_phylum) <- phyloseq::tax_table(ps_phylum)[, "class/order/family/genus"]

phyloseq::psmelt(ps_phylum) %>%
ggplot(data = ., aes(x = Status, y = Abundance)) +
  geom_boxplot(outlier.shape  = NA) +
  geom_jitter(aes(color = OTU), height = 0, width = .2) +
  labs(x = "", y = "Abundance\n") +
  facet_wrap(~ Phylum, scales = "free")