Create a new RStudio project
Open RStudio and create a new project, for more info see https://support.rstudio.com/hc/en-us/articles/200526207-Using-Projects
- File > New Project > New Directory > New Project (name the new directory, Ex. Data_in_R) and check “use packrat with this project” if present.
Learn more about packrat see https://rstudio.github.io/packrat/
Set some options and make sure the packages ‘knitr’, ‘tidyverse’, ‘reshape2’, and ‘gr are installed (if not install it), and then load
In the R console run the following commands
if (!any(rownames(installed.packages()) == "knitr")){
install.packages("knitr")
}
library(knitr)
if (!any(rownames(installed.packages()) == "tidyverse")){
install.packages("tidyverse")
}
library(tidyverse)
if (!any(rownames(installed.packages()) == "reshape2")){
install.packages("reshape2")
}
library(reshape2)
if (!any(rownames(installed.packages()) == "gridExtra")){
install.packages("gridExtra")
}
library(gridExtra)
Learn more about the tidyverse see https://www.tidyverse.org.
Open a new R Notebook
An R notebook is an R Markdown document with chunks that can be executed independently and interactively, with output visible immediately beneath the input. More info see https://rmarkdown.rstudio.com/r_notebooks.html
- File -> New File -> R Notebook
- Save the Notebook (Ex. test)
R Markdown
This is an R Markdown document. Markdown is a simple formatting syntax for authoring HTML, PDF, and MS Word documents. For more details on using R Markdown see http://rmarkdown.rstudio.com.
When you click the preview or Knit button a document will be generated that includes both content as well as the output of any embedded R code chunks within the document. You can embed R code and plots in chunks like this:
```{r chunk_name}
print('hello world!')
```
Review the R Markdown page and R Markdown cheat sheets.
Try ‘knitting’ to html, pdf, and doc as well as previewing the notebook. Open the resulting documents.
Try executing the code chunks in the R Notebook.
Download the data file for the workshop document and preview/open it
This is the stats file generated after running samtools stats on a bam file generated from running BWA MEM.
In the R console run the following command.
download.file("https://raw.githubusercontent.com/ucdavis-bioinformatics-training/2019_August_UCD_mRNAseq_Workshop/master/intro2R/Data_in_R_files/bwa_mem_Stats.log", "bwa_mem_Stats.log")
Download the template Markdown workshop document and open it
In the R console run the following command
download.file("https://raw.githubusercontent.com/ucdavis-bioinformatics-training/2019_August_UCD_mRNAseq_Workshop/master/intro2R/data_in_R.Rmd", "data_in_R.Rmd")
Edit the file YAML portion
The top YAML (YAML ain’t markup language) portion of the doc tells RStudio how to parse the document.
---
title: "Data_in_R"
author: your_name
date: current_date
output:
html_notebook: default
html_document: default
---
What are we going to do?
We will recreate some of the plots generated with plot-bamstats on the same file
You can view the output of plot-bamstats -> bwa_mem_stats.html