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
R basics
4.1
Arithmetic operators
4.2
Simple calculations
4.3
Objects in R
4.4
Assignment operators
4.5
Assigning data to an object
4.6
Using objects
4.7
Names of objects
5
Paths and directories
5.1
Tree of directories
5.2
Navigate the tree of directory with the R console
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 ~ 10 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 (15 minutes)
9.2.1
Exercise 2a.
9.2.2
Exercise 2b.
9.3
Exercise 3. Character vector manipulation (10 minutes)
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
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 6: about Module 2…
12.9
Workspace
12.10
Exercise 7. Input / output and data selection.
12.10.1
Exercise 7
13
“Base” plots in R
13.1
Scatter plots
13.2
Bar plots
13.3
Pie charts
13.4
Box plots
13.5
Histograms
14
How to save plots
14.1
With R Studio
14.2
With the console
14.3
Exercise 8: Base plots
14.3.1
Exercise 8a- scatter plot
14.3.2
Exercise 8b- bar plot + pie chart
14.3.3
Exercise 8c- histogram
15
Plots from other packages
15.1
pheatmap function from the pheatmap package
15.2
venn.diagram function from VennDiagram package
16
ggplot2 package
16.1
Getting started
16.2
Scatter plot
16.3
Box plots
16.4
Bar plots
16.4.1
Bar plots with error bars
16.5
Histograms
16.6
About themes
16.7
Saving plots in files
16.8
Exercise 9: ggplot2
16.8.1
Exercise 9a- Scatter plot
16.8.2
Exercise 9b- Box plot
16.8.3
Exercise 9c- Bar plot
16.8.4
Exercise 9d- Histogram
16.9
More about the theme() function
16.10
demo: volcano plots
17
Regular expressions
17.1
Find simple matches with grep
17.2
Regular expressions to find more flexible patterns
17.3
Substitute or remove matching patterns with gsub
17.4
Predefined variables to use in regular expressions:
17.5
Use grep and regular expressions to retrieve columns by their names
17.6
Exercise 10: Regular expressions
18
Conditional statement
18.1
Exercise 11: If statement
19
Repetitive execution
19.1
Exercise 12: For loop
Published with bookdown
Introduction to R (2021)
Part 15
Plots from other packages
We will see two additional types of plots:
Heat map (from package pheatmap)
Venn diagram (from package VennDiagram)