Alpha多样性指数稀释曲线绘制

首先利用qiime diversity alpha-rarefaction命令进行Alpha多样性指数稀释曲线分析，具体用法参考qiime2官方文档。

结果如下图所示：

qiime2 alpha-rarefaction

上面的结果比较简陋，使用qiime tools export命令或者解压缩从结果导出数据以便于在R中分析，导出文件如下图所示

导出的文件（红框中是要使用的数据）

使用如下代码绘制稀释曲线

```

library(tidyverse)

data <- read_csv("observed_otus.csv")

data2 <- data %>% gather("depth", "observed_otus", -`sample-id`, -Group) %>%

  mutate(depth = str_replace(depth, "_iter\\-\\d+", "")) %>%

  mutate(depth = as.numeric(str_replace(depth, "depth\\-", ""))) %>% na.omit()

p1 <- ggplot(data2, aes(depth, observed_otus, color = Group, group = `sample-id`))+

  geom_smooth(se = FALSE, method = "lm", formula = y~log(x))

ggsave("observed_otus_rarefaction_samples.png", height = 5, width = 8)

p2 <- ggplot(data2, aes(depth, observed_otus, color = Group, group = Group))+

  geom_smooth(se = FALSE, method = "lm", formula = y~log(x))

ggsave("observed_otus_rarefaction_groups.png", height = 5, width = 8)

```

结果如下：

data2数据概览

data2

observed_otus Rarefaction Curves

observed_otus Rarefaction Curves - samples observed_otus Rarefaction Curves - groups