MicrobiotaProcess-basics.Rmd

---
title: "basics analysis using MicrobiotaProcess"
author: |
  | Shuangbin Xu 
  | School of Basic Medical Sciences, Southern Medical University
date: "`r Sys.Date()`"
bibliography: MicrobiotaProcess.bib
biblio-style: apalike
output:
  prettydoc::html_pretty:
    toc: true
    theme: cayman
    highlight: vignette
  pdf_document:
    toc: true
vignette: >
  %\VignetteIndexEntry{ MicrobiotaProcess: basics analysis using MicrobiotaProcess.}
  %\VignetteEngine{knitr::rmarkdown}
  %\usepackage[utf8]{inputenc}
  %\VignetteEncoding{UTF-8}
---

```{r, echo=FALSE, results="asis", message=FALSE, KnitrSetUp}
knitr::opts_chunk$set(tidy=FALSE,warning=FALSE,message=FALSE)
Biocpkg <- function (pkg){
    sprintf("[%s](http://bioconductor.org/packages/%s)", pkg, pkg)
}

CRANpkg <- function(pkg){
    cran <- "https://CRAN.R-project.org/package" 
    fmt <- "[%s](%s=%s)"
    sprintf(fmt, pkg, cran, pkg) 
}
```

```{r, echo=FALSE, results="hide", message=FALSE, Loadpackages}
library(ggplot2)
library(DT)
library(tidyverse)
library(phyloseq)
library(ggtree)
library(treeio)
library(tidytree)
library(MicrobiotaProcess)
```

# 1. Introduction

`MicrobiotaProcess` is an R package for analysis, visualization and biomarker discovery of microbial datasets. It supports the import of microbiome census data, calculating alpha index and provides functions to visualize rarefaction curves. Moreover, it also supports visualizing the abundance of taxonomy of samples. And It also provides functions to perform the `PCA`, `PCoA` and hierarchical cluster analysis. In addition, `MicrobiotaProcess` also provides a method for the biomarker discovery of metagenome or other datasets.

# 2. `MicrobiotaProcess` profiling

## 2.1 import function

`MicrobiotaProcess` has an feature to import phylogenetic sequencing data from `r Biocpkg("dada2")`[@callahan2016dada2] and [qiime2](https://qiime2.org/)[@bolyen2019qiime2] taxonomic clustering pipelines. The resulting object after import is `r Biocpkg("phyloseq")` object[@Paul2013phyloseq]

```{r, error=FALSE, importFunction}
# import data from dada2 pipeline.
seqtabfile <- system.file("extdata", "seqtab.nochim.rds", package="MicrobiotaProcess")
seqtab <- readRDS(seqtabfile)
taxafile <- system.file("extdata", "taxa_tab.rds",package="MicrobiotaProcess")
seqtab <- readRDS(seqtabfile)
taxa <- readRDS(taxafile)
# the seqtab and taxa are output of dada2
sampleda <- system.file("extdata", "mouse.time.dada2.txt", package="MicrobiotaProcess")
ps_dada2 <- import_dada2(seqtab=seqtab, taxatab=taxa, sampleda=sampleda)
ps_dada2

# import data from qiime2 pipeline
otuqzafile <- system.file("extdata", "table.qza", package="MicrobiotaProcess")
taxaqzafile <- system.file("extdata", "taxa.qza", package="MicrobiotaProcess")
mapfile <- system.file("extdata", "metadata_qza.txt", package="MicrobiotaProcess")
ps_qiime2 <- import_qiime2(otuqza=otuqzafile, taxaqza=taxaqzafile, mapfilename=mapfile)
ps_qiime2
```

## 2.2 Rarefaction visualization

Rarefaction, based on sampling technique, was used to compensate for the effect of sample size on the number of units observed in a sample[@siegel2004rarefaction]. `MicrobiotaProcess` provided `ggrarecurve` to plot the curves, based on `rrarefy` of `r CRANpkg("vegan")`[@Jari2019vegan].

```{r, error=FALSE, fig.align="center", fig.height=3.2, fig.width=7.5, rarefaction}
# for reproducibly random number 
set.seed(1024)
p_rare <- ggrarecurve(obj=ps_dada2, 
                      indexNames=c("Observe","Chao1","ACE"), 
                      chunks=300) +
          theme(legend.spacing.y=unit(0.02,"cm"),
                legend.text=element_text(size=6))
p_rare

```

## 2.3 calculate alpha index and visualization

`MicrobiotaProcess` provides `get_alphaindex` to calculate alpha index and the `ggbox` to visualize the result

```{r, error=FALSE, fig.width=7.5, fig.height=3.2, fig.align="center", alphaindex}
alphaobj <- get_alphaindex(ps_dada2)
head(as.data.frame(alphaobj))
p_alpha <- ggbox(alphaobj, geom="violin", factorNames="time") + 
	scale_fill_manual(values=c("#2874C5", "#EABF00"))+
	theme(strip.background = element_rect(colour=NA, fill="grey"))
p_alpha
```

## 2.4 The visualization of taxonomy abundance

`MicrobiotaProcess` presents the `ggbartax` for the visualization of composition of microbial communities.

```{r, error=FALSE, fig.align="center", fig.height=4.5, fig.width=7, taxabar}
# relative abundance
otubar <- ggbartax(obj=ps_dada2) +
	  xlab(NULL) +
	  ylab("relative abundance (%)")
otubar
```

If you want to get the abundance of specific levels of class, You can use `get_taxadf` then use `ggbartax` to visualize.

```{r, error=FALSE, fig.align="center", fig.height=4.5, fig.width=7, phylumAbundance}
phytax <- get_taxadf(obj=ps_dada2, taxlevel=2)
phybar <- ggbartax(obj=phytax) +
          xlab(NULL) + ylab("relative abundance (%)")
phybar
```

 Moreover, the abundance (count) of taxonomy also can be visualized by setting count to TRUE, and the facet of plot can be showed by setting the facetNames.

```{r, error=FALSE, fig.align="center", fig.height=4.5, fig.width=7, classAbundance}
phybar2 <- ggbartax(obj=phytax, facetNames="time", count=TRUE) + xlab(NULL) + ylab("abundance")
phybar2
classtax <- get_taxadf(obj=ps_dada2, taxlevel=3)
classbar <- ggbartax(obj=classtax, facetNames="time", count=FALSE) +
                xlab(NULL) + ylab("relative abundance (%)")
classbar
```

## 2.5 PCA and PCoA analysis

`PCA` (Principal component analysis) and `PCoA` (Principal Coordinate Analysis) are general statistical procedures to compare groups of samples. And `PCoA` can based on the phylogenetic or count-based distance metrics, such as `Bray-Curtis`, `Jaccard`, `Unweighted-UniFrac` and `weighted-UniFrac`. `MicrobiotaProcess` presents the `get_pca`, `get_pcoa` and `ggordpoint` for the analysis.

```{r, error=FALSE, fig.align="center", fig.height=4.5, fig.width=6, ordanalysis}
pcares <- get_pca(obj=ps_dada2, method="hellinger")
# Visulizing the result
pcaplot <- ggordpoint(obj=pcares, biplot=TRUE, speciesannot=TRUE,
                      factorNames=c("time"), ellipse=TRUE) + 
           scale_color_manual(values=c("#2874C5", "#EABF00"))
pcaplot

pcoares <- get_pcoa(obj=ps_dada2, distmethod="euclidean", method="hellinger")
# Visualizing the result
pcoaplot <- ggordpoint(obj=pcoares, biplot=TRUE, speciesannot=TRUE,
                       factorNames=c("time"), ellipse=TRUE) +
            scale_color_manual(values=c("#2874C5", "#EABF00"))
pcoaplot
```

## 2.6 Hierarchical cluster analysis

`beta diversity` metrics can assess the differences between microbial communities. It can be visualized with `PCA` or `PCoA`, this can also be visualized with hierarchical clustering. `MicrobiotaProcess` also  implements the analysis based on ggtree[@yu2017ggtree].

```{r, fig.align="center", fig.height=5, fig.width=6, error=FALSE, hclustAnalysis}
hcsample <- get_clust(obj=ps_dada2, distmethod="euclidean",
		      method="hellinger", hclustmethod="average")
# rectangular layout
clustplot1 <- ggclust(obj=hcsample,
                      layout = "rectangular",
                      pointsize=1,
                      fontsize=0,
                      factorNames=c("time")) +
              scale_color_manual(values=c("#2874C5", "#EABF00")) +
              theme_tree2(legend.position="right",
                          plot.title = element_text(face="bold", lineheight=25,hjust=0.5))
clustplot1
# circular layout
clustplot2 <- ggclust(obj=hcsample,
                      layout = "circular",
                      pointsize=1,
                      fontsize=2,
                      factorNames=c("time")) +
              scale_color_manual(values=c("#2874C5", "#EABF00")) +
              theme(legend.position="right")
clustplot2
```

# 3. Need helps?

If you have questions/issues, please visit [github issue tracker](https://github.com/YuLab-SMU/MicrobiotaProcess/issues).

# 4. Session information

Here is the output of sessionInfo() on the system on which this document was compiled:

```{r, echo=FALSE}
sessionInfo()
```

# 5. References