R introduction

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This material is linked to an online training. Most of the theory can be found here on the e-learning system. The online sessions repeat the theory and are mostly intended to get practical experience.

Material

Tutorial with the exercises
Folder with the data sets

Software

R
RStudio
Install R and RStudio on Mac: video tutorial created by Gunesh Shanbhag on installing R and RStudio on Mac and short overview of the RStudio user interface on Mac.

External links

External links for graphing

hexadecimal color codes
names of the colors
names and numbers of lines and shapes
examples of graphs (all graphing systems)
online book on ggplot2
ggplot2 tutorial

Course Content

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Rstudio user interface 5 Topics

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Script editor and console

Files tab: setting the working directory

Packages tab: installing packages

Help tab: getting help

Basic syntax in R 1 Quiz

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Comparisons in R 2 Topics | 1 Quiz

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Logical operators

Logical operations

Combine logical operations

Creating variables 4 Topics | 2 Quizzes

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Create variables by assigning a value

Create variables by running a function

Running functions

Using multiple functions after each other

Functions with the same name from different packages

Vectors 4 Topics | 4 Quizzes

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Create a vector

How to create vectors?

Retrieve elements from a vector

How to retrieve elements?

Change or remove elements from a vector

How to remove and change elements?

Logical and arithmetic operations on variables

Logical operation on a vector

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Order of levels

Matrices 1 Quiz

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Retrieving elements from a matrix

Data frames 4 Topics | 2 Quizzes

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Create a data frame

Retrieve elements from a data frame

How to retrieve elements from a data frame?

Remove columns from a data frame

How to change elements in a data frame?

Add and reorder columns in a data frame

Operations on variables 9 Topics | 5 Quizzes

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Mathematical functions for vectors and tables

Mathematical functions

Functions for tables: names of rows/columns and merging

Functions on tables

Functions that work on text

Functions that work on factors

Sort versus order

Functions that return indices

Functions that return indices

Functions to check and change the type of variables

Type of variable?

Functions for handling missing values

How to remove missing values?

Operations on rows of tables are hard

Reading and writing files 5 Topics | 1 Quiz

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Define the file you want to read

The read functions

Arguments of the read functions

Reading compressed files

Calculate descriptive statistics 3 Topics | 3 Quizzes

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Calculate descriptive statistics

Descriptive statistics

apply() as a substitute for for-loops in R

Calculate statistics per group

How to select columns with dplyr?

Get your data in the right format 1 Quiz

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How to make a formula for dcast()?

Conditional statements 1 Quiz

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How does ifelse() work?

Using annotation to map IDs

Fetch data from NCBI 3 Topics | 1 Quiz

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Search NCBI databases

Search NCBI databases

Check links in NCBI

Fetch the data from NCBI

Make graphs with ggplot2 16 Topics | 11 Quizzes

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Define what you want to plot

How to make a plot with 2 factors?

Define what you want to plot for a plot with 2 factors

The philosophy behind ggplot2

Plot statistics with stat_summary()

How to plot bars that represent a mean?

Why factor() is important in plots

Plot the data with geoms

Arguments to set colors, shapes, line types, position…

Position on a plot

Plots with points: scatter, bubble, hexbin and beeswarm plots

Plots with bars and points

Plot distributions: histogram, QQ, box, violin and ridge plots

Adding lines to a plot

Regression lines

Adding text labels to a plot

Add text labels

Adding titles to a plot

Scales define what the axes and the legend look like

Themes define all remaining characteristics of a plot

Combine multiple plots on a graph 3 Topics | 1 Quiz

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Facets: multiple plots of the same type on one graph

ggarrange: multiple different plots on the same graph

gridExtra: plots and tables on the same graph

Multiple plots on a graph

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