cheatsheet.Rmd

---
title: "Introduction to R for Biologists cheatsheet"
author: "Maria Doyle"
date: "`r format(Sys.time(), '%d %B %Y')`"
output:
  pdf_document:
    toc: no
  html_notebook:
    toc: yes
    toc_depth: 4
    toc_float: yes
subtitle: glossary of vocabulary used in the course
---

## Packages

**dplyr**  
tidyverse package for manipulating data, contains the `mutate()`, `filter()`, `select()`, `full_join()` functions and includes the `%>%` operator (from the magrittr package)

**ggplot2**  
tidyverse package for data visualisation 

**readr**  
tidyverse package for reading data into R, contains the `read_tsv()` function

**tidyr**  
tidyverse package for data tidying, contains the `pivot_longer()` function

**tidyverse**  
a collection of packages that work together for data reading, tidying, manipulating and visualising


\ 


## Functions

**`c()`**  
combine values (from base R)  
  
**`case_when()`**  
test multiple conditions (from dplyr), useful inside `mutate()` when creating columns
  
**`colnames()`**  
access column names (from base R)
  
**`colours()`**  
see the built-in R colours (from base R)
  
**`dev.off()`**  
turn off the R graphics device (from base R). Used after e.g. `pdf()`, `png()`.
  
**`dim()`**  
retrieve the dimensions of an object, for example, the number of rows and columns (from base R)
  
**`factor()`**  
convert values to factor data type (from base R)

**`filter()`**  
choose rows (from dplyr)

**`full_join()`**  
joins 2 tables returning all rows and all columns from both tables.

**`getwd()`**  
find out what the working directory is (get working directory)

**`ggplot()`**  
function used to create a ggplot (from ggplot2)

**`head()`**  
selecting the first part of an object (from base R). Default is to show the first 6 items.

**`labs()`**  
modify title, axis and legend labels on a ggplot (from ggplot2)

**`levels()`**  
retrieve the levels (category names) of a factor (from base R)

**`library()`**  
load packages (from base R)

**`log2()`**  
compute the log2 (base 2) logarithms (from base R)

**`mutate()`**  
add columns (from dplyr)

**`pdf()`**  
create a pdf, used with `dev.off()` (from base R)

**`pivot_longer()`**  
function that enables converting from wide to long (tidy) format (from dplyr)

**`pull()`**  
extract values e.g. out of a column (from dplyr)

**`read_csv()`**  
read a comma-separated file into R (from readr)

**`read_tsv()`**  
read a tab-separated file into R (from readr)

**`select()`**  
choose columns (from dplyr)

**`str()`**  
showing the structure of an object (from base R). Useful for checking data types.

**`summary()`**  
producing a summary of an object (from base R). Useful for getting summary statistics of numeric columns (min, max, mean, median)

**`tail()`**  
selecting the last part of an object (from base R). Default is to show the last 6 items.

**`View()`**  
invoke a spreadsheet-like viewer on an R object (from base R)


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## Terms

**argument**  
an input to a function

**assignment operator**  
`<-` assigns values to objects, assigns a value on the right to an object on the left (from base R) 

**character**  
a data type in R, used to represent character strings, quotes indicate the data type is character

**console**  
a window where you can interactively type in commands and the output is returned

**double**  
a data type in R, used to represent numbers containing a decimal point (integer is the data type for numbers without decimal point)

**factor**  
a data type in R, used to represent categories

**function**   
a pre-defined set of commands used to perform a task, can be loaded in from packages or user-created

**geom**  
type of ggplot e.g. `geom_line()`, `geom_point()`, `geom_jitter()`, `geom_boxplot()`, `geom_violin()`

**object**  
everything in R is an object. The assignment operator `<-` can be used to create objects. Note that what R calls objects are called variables in other languages such as Python.

**package**  
a package is a collection of functions and usually includes code, documentation, tests and example datasets.

**pipe**  
`%>%` operator chains together tidyverse commands (from the magrittr package)

**scales**  
scale_fill_manual(), scale_colour_manual(), scale_fill_brewer(), scale_colour_brewer(). Use to specify colours.

**script**  
a text file containing commands, in R a script filename ends with .R

**themes**  
the non-data components of a ggplot e.g. background, grid lines, font size and font type

**working directory**  
the location (path) where R looks to read in data and save files

\ 

##Symbols##

**`>`**  
prompt in console, means R is ready to take a command
   
\    
**`+`**  
used to add layers to a ggplot. Also the prompt symbol R uses when the command is not complete, such as missing a `)`
  
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**`<-`**  
assignment operator, see Terms above  

\    
**`#`**  
comment, to add notes to a script  
  
\   
**`$`**  
way to access a single column with base R e.g. `counts$gene_symbol`  
  
\   
**`%in%`**  
operator used to test if a value is in a set of values  
  
\   
**`%>%`**  
dplyr pipe operator, see Terms above  
  
\   
**`~`**  
symbol to use when faceting in ggplot2, used to indicate the column to use to facet