Introduction to R
1
Welcome
2
What is R ?
3
What is RStudio ?
3.1
RStudio access
3.2
RStudio interface
3.3
Setting up the folder structure for the course
3.3.1
Note on files and folders names
4
Paths and directories
4.1
Tree of directories
4.2
Navigate the tree of directory with the R console
5
R basics
5.1
Arithmetic operators
5.2
Simple calculations
5.3
Objects in R
5.4
Assignment operators
5.5
Assigning data to an object
5.6
Names of objects
6
Functions
7
R scripts
7.1
Create and save a script
7.2
R syntax
7.3
RStudio tips in the console
7.4
Exercice 1. Getting started ~ 15 minutes
8
Data types
8.1
Checking data types
9
Data structures
9.1
Vectors
9.1.1
Creating a vector
9.1.2
Vector manipulation
9.1.3
Combining vectors
9.1.4
Numeric vector manipulation
9.1.5
Character vector manipulation
9.2
Exercise 2. Numeric vector manipulation
9.2.1
Exercise 2a.
9.2.2
Exercise 2b.
9.3
Exercise 3. Character vector manipulation
9.3.1
Exercise 3a.
9.3.2
Exercise 3b.
9.4
Factors
9.5
Matrices
9.5.1
Creating a matrix
9.5.2
Two-dimensional object
9.5.3
Matrix manipulation
9.6
Data frames
9.6.1
Create a data frame
9.6.2
Data frame manipulation:
9.7
Two-dimensional structures manipulation
9.7.1
Dimensions
9.7.2
Manipulation
9.8
Exercise 4. Matrix manipulation
9.9
Exercise 5. Data frame manipulation
9.9.1
Exercise 5a
9.9.2
Exercise 5b
9.9.3
Exercise 5c
10
Missing values
11
Input / Output
11.1
On vectors
11.2
On data frames or matrices
11.3
Exercise 6.
11.3.1
Exercise 6a. Input / output
11.3.2
Exercise 6b - I/O on data frames: play with the arguments of read.table
12
Library and packages
12.1
R base
12.2
R contrib
12.3
Install a package
12.4
Load a package
12.5
Check what packages are currently loaded
12.6
List functions from a package
12.7
RStudio server at CRG
12.8
Exercise 7: Library and packages
12.9
Exercise (to do at home)
13
Regular expressions
13.1
Find simple matches with grep
13.2
Regular expressions to find more flexible patterns
13.3
Substitute or remove matching patterns with gsub
13.4
Predefined variables to use in regular expressions:
13.5
Use grep and regular expressions to retrieve columns by their names
13.6
Exercise 8: Regular expressions
14
Conditional statement
14.1
Exercise 9: If statement
15
Repetitive execution
15.1
Exercise 10: For loop
16
“Base” plots in R
16.1
Scatter plots
16.2
Bar plots
16.3
Pie charts
16.4
Box plots
16.5
Histograms
17
How to save plots
17.1
With R Studio
17.2
With the console
17.3
Exercise 11: Base plots
17.3.1
Exercise 11a- scatter plot
17.3.2
Exercise 11b- bar plot + pie chart
17.3.3
Exercise 11c- histogram
18
Plots from other packages
18.1
heatmap.2 function from gplots package
18.2
pheatmap function from the pheatmap package
18.3
venn.diagram function from VennDiagram package
19
ggplot2 package
19.1
Getting started
19.2
Scatter plot
19.3
Box plots
19.4
Dot plots
19.5
Bar plots
19.5.1
Bar plots with error bars
19.6
Histograms
19.7
About themes
19.8
Saving plots in files
19.9
Exercise 12: ggplot2
19.9.1
Exercise 12a- Scatter plot
19.9.2
Exercise 12b- Box plot
19.9.3
Exercise 12c- Bar plot
19.9.4
Exercise 12d- Histogram
19.10
More about the theme() function
19.11
Volcano plots
Published with bookdown
Introduction to R
Part16
“Base” plots in R
R-base package graphics offers functions for producing many plots, for example:
scatter plots - plot()
bar plots - barplot()
pie charts - pie()
box plots - boxplot()
histograms - hist()