Introduction into R markdown

Creating an R Markdown file

Each R markddown file contains three types of text:

• An (optional) YAML header surrounded by —s
• R code chunks surrounded by ```s
• text mixed with simple text formatting

YAML header

• title: “….”
• author: “….”
• date: “….”
• output: html_document/pdf_document/word_document

Plain text

formating is done using marks
# Header
## Header 2

bold with double-asterisks
italics with underscores
code-type font with backticks

Chunk options

write in the bracketes after letter “r” or as general statment e.g. knitr::opts_chunk$set(echo = TRUE) on the beginning

• include = FALSE prevents code and results from appearing in the finished file. R Markdown still runs the code in the chunk, and the results can be used by other chunks.
• echo = FALSE prevents code, but not the results from appearing in the finished file. This is a useful way to embed figures.
• message = FALSE prevents messages that are generated by code from appearing in the finished file.
• warning = FALSE prevents warnings that are generated by code from appearing in the finished.
• fig.cap = “…” adds a caption to graphical results.
• fig.height, fig.width
• results = “markpup” or “asis” or “hide” or “hold”

Inside chunk

Sometimes is good to have formated text also inside the chunks e.g. when you create the figures or data analysis by loop

• cat start for header
• knitr::kable() formated table

Printing the table

ID	strain	sex	group	cohort
064-EPL19	2510009E07Rik (indel)	Male	Male KO_E07Rik	c007
064-EPL20	2510009E07Rik (indel)	Male	Male KO_E07Rik	c007
064-EPL40	2510009E07Rik (indel)	Male	Male KO_E07Rik	c007
064-EPL69	2510009E07Rik (indel)	Male	Male KO_E07Rik	c007
064-EPL75	2510009E07Rik (indel)	Male	Male KO_E07Rik	c007

Plotting the data and save them

Tasks

1. Write a sentence containing words with bold, italics, and underlined formatting.
2. Create a plot generated with 3 inches wide and 5 inches high
3. test different Chunk options for final document