phyloseq_2_Example Data in phyloseq.Rmd

---
title: "phyloseq_2_Example Data in phyloseq"
author: "wentao"
date: "2019/8/23"
output: html_document
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(
	echo = TRUE,
	message = FALSE,
	warning = FALSE
)
```

# phyloseq示例
**Example Data in phyloseq**

ggplot2包主题设置。更多帮助，请参阅ggplot2联机文档。

><font size=2>ggplot2 package theme set. See the ggplot2 online documentation for further help.</font>

```{R}
library("phyloseq"); packageVersion("phyloseq")
library("ggplot2"); packageVersion("ggplot2")
theme_set(theme_bw())

```


phyloseq中自带有多份数据，许多来自发表的文献
><font size=2>There are multiple example data sets included in phyloseq. Many are from published investigations and include documentation with a summary and references, as well as some example code representing some aspect of analysis available in phyloseq.</font>

data()函数将数据载入到R的环境中。

><font size=2>To load example data into the working environment, use the data() command:</font>

```{R}

#使用phyloseq
data(GlobalPatterns)
data(esophagus)
data(enterotype)
data(soilrep)

```

### 文档
**Documentation**

在包索引目录中，转到以“data”开头的名称以查看当前可用示例数据集的文档。

><font size=2>In the package index, go to the names beginning with “data-” to see the documentation of currently available example datasets.</font>

查看GlobalPatterns数据介绍
```{R eval=FALSE, include=FALSE}
# ?GlobalPatterns

```
浏览GlobalPatterns数据集

><font size=2>to access the documentation for the so-called “GlobalPatterns” dataset</font>

####  调用数据：测试一个例子文件
*Run provided examples*

可以使用r中的example命令来展示示例数中包含的例子（以及函数/方法的示例），在本例中是enterotype数据集

><font size=2>You can also try the examples included with the example data documentation (as well as examples for functions/methods) using the standard example command in R – in this case the examples for the enterotype dataset</font>

```{R}
example(enterotype, ask=FALSE)

# ?example
```

example 命令拆分，即为一下三条命令

```{R}
data(enterotype)
ig <- make_network(enterotype, "samples", max.dist=0.3)

plot_network(ig, enterotype, color="SeqTech", shape="Enterotype", line_weight=0.3, label=NULL)
```


### reference
https://joey711.github.io/phyloseq/Example-Data.html