Microbes on Earth - ES2304 & ES7027

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# Microbes on Earth

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## R - installation and reading

.font120[**Daniel Vaulot**]

2021-10-12

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# Outline

.font150[
* [Session 01 - Introduction to R](https://daniel-vaulot.fr/html/course-microbes-2021/R-session-01-intro.html)
* [Session 02 - Data wrangling](https://daniel-vaulot.fr/html/course-microbes-2021/R-session-02-data_wrangling.html)
* [Session 03 - Data viz](https://daniel-vaulot.fr/html/course-microbes-2021/R-session-03-data_visualization.html)
* [Session 04 - R markdown](https://daniel-vaulot.fr/html/course-microbes-2021/R-session-04-markdown.html)
* [Session 05 - Metabarcode analyses with Phyloseq](https://daniel-vaulot.fr/html/course-microbes-2021/R-session-05-phyloseq.html) 
]

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# Installation

## R and R packages

* Install [R](https://cran.r-project.org/index.html)

* Install [R studio](https://www.rstudio.com/products/rstudio/download/#download)

* Install the following packages
  * Data manipulation
    * **readxl**  : Reading Excel files
    * **readr**   : Reading and writing Text files
    * **dplyr** : Filter and reformat data frames
    * **tidyr** : Make data "tidy"
    * **tibble** : Manipulate data frames
    * **stringr** :  Manipulating strings
  * Graphics
    * **ggplot2**: Graphics
  * Markdown
    * **knitr**
    * **tinytex**
  * Metabarcode analysis
    * **[phyloseq](https://bioconductor.org/packages/release/bioc/html/phyloseq.html)**
  
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# Reading material
##  Session 01-03 - Data analysis

Choose of the two text below. Make sure you make the exercises.

* [Statistical Inference via Data Science](https://moderndive.netlify.app/index.html)
  * Chapters 1 to 3

* [R for Data Science](https://r4ds.had.co.nz/)
  * Chapters 1 to 5
  * [Solutions to exercises](https://jrnold.github.io/r4ds-exercise-solutions)

## Session 04 - Rmarkdown
* [Intro to R markdown](https://ourcodingclub.github.io/tutorials/rmarkdown/)

## Session 05 - Phyloseq

* [Phyloseq paper](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0061217)
* [Phyloseq help](https://joey711.github.io/phyloseq/index.html) - see Tutorials

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# Installation - MetaPR2 package

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## Step 1 - Download the R package

[https://daniel-vaulot.fr/html/course-microbes-2021/metapr2-shiny-main.zip](https://daniel-vaulot.fr/html/course-microbes-2021/metapr2-shiny-main.zip)

## Step 2 - Install package on your computer

* Unpack Zip file

* Launch shiny_metapr2.Rproj

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## Step 3 - Install the following libraries

```r
### Shiny
install.packages("shiny" ) 
install.packages("shinyvalidate" ) # For validation of input (easier to use than shinyFeedback)
install.packages("shinycssloaders" ) # For the spinning wheel
install.packages("shinyWidgets" ) # for Extra widgets - https://dreamrs.github.io/shinyWidgets/index.html
install.packages("markdown" ) # To display text boxes in md
install.packages("DT" ) # For table display

### Tidyverse
install.packages("dplyr" )
install.packages("tidyr" )
install.packages("stringr" )
install.packages("forcats" )
```

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## Step 3 - Install the following libraries

```r
### graphics
install.packages("ggplot2" )
install.packages("viridis" )
install.packages("patchwork" )
install.packages("treemapify" )

### maps
install.packages("leaflet" )
install.packages("leaflet.minicharts" ) # To do nice pie charts

### Misc
install.packages("rio" )

### Bioinformatics

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("Biobase")
BiocManager::install("Biostrings")
BiocManager::install("phyloseq")
```

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## Step 4 - Launch the metaPR2 shiny server

Run the following line from R studio

```r
install.packages("pkgload")

pkgload::load_all(".")

metapr2App()
```

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## Stop the Shiny application

* Close the browser window

* Hit the stop button at the top right of the bottom left window

## In case Shiny application crashes

* Hit the stop button at the top right of the bottom left window
* Relaunch `metapr2App()`