Visualization in R
1
About
2
Hello World - base R
2.1
Welcome
2.1.1
Interacting with R
2.1.2
Chunks
2.2
Test ‘knitting’
2.3
Resources on R
3
Importing data - base R
3.1
Using base R
3.1.1
Tab-delimited data with a header and using standard decimal points
3.1.2
Non-standard decimal points
3.1.3
Comma-separated data with a header and using standard decimal points
3.1.4
Tables without headers
3.1.5
Additional lines
3.2
Further methods
3.2.1
Excel files
3.2.2
Reading from URLs
3.2.3
Reading from the clipboard
4
Intro to the {tidyverse}
4.1
Why
{tidyverse}
?
4.2
Reading data from excel
4.3
The pipe operator
4.4
Resources on tidyverse
5
Introduction to scatter plots in base R
5.1
Set up
5.2
Formatting plots
5.2.1
Defaults
5.2.2
Margins
5.2.3
Plot borders
5.3
Axes
5.3.1
Axis marks
5.3.2
Axis labels
5.3.3
Scales and ranges
5.4
Points
5.4.1
Shapes
5.4.2
Colour
5.4.3
Size
5.4.4
Multiple sets of points
5.5
Legends
5.6
Lines
5.6.1
Histogram-style lines
5.6.2
Lines between points
5.6.3
Lines through the plot
5.6.4
Trend lines
6
Introduction to scatter plots in R/ggplot2
6.1
Setup
6.2
Scatterplots
6.2.1
Defaults
6.2.2
Themes
6.3
Intermezzo: Plots as objects
6.4
Modifying plots
6.4.1
Axis labels
6.4.2
Scales and ranges
6.4.3
Aesthetics & Geometries
6.5
Legends
6.6
Lines and trends
7
Summarizing distributions in base R
7.1
Setup
7.2
The data
7.3
Just the mean: Barplots
7.3.1
Simple barplots
7.3.2
Barplots with error bars
7.4
Medians, quartiles, and outliers: Boxplots
7.4.1
Basic boxplots
7.4.2
Adding points on top
7.4.3
Adding lines between points
7.4.4
Half-boxes
7.5
Histograms
7.6
Density plots
7.7
Violinplots
7.8
Beanplots
8
Distributions & ggplot2
8.1
Setup and data
8.2
Multiple distributions
8.2.1
Plotting the data
8.3
Boxplots
8.4
Violinplots
8.5
Facets: Splitting into multiple plots
8.6
A single distribution
8.6.1
A single violinplot
8.6.2
Density plot
8.6.3
Histogram
8.7
Two distributions
8.7.1
Histogram & Density
8.7.2
Splitting into two plots
9
Heatmaps
et al.
- base R
9.1
Setup
9.2
Loading data
9.3
Basic heatmaps
9.3.1
A simple heatmap
9.3.2
Scaling
9.3.3
Colour schemes
9.4
Decorating heatmaps
9.4.1
Dendrograms
9.4.2
Ordering features and samples
9.4.3
Adding attributes
10
Venn, Euler, and upSet diagrams
10.1
Setup and data
10.2
Venn diagrams
10.3
Euler diagrams
10.4
UpSet plots
11
Visualizing networks with igraph
11.1
Setup
11.2
Network representations
11.2.1
Network formats: edgelist
11.2.2
Network formats: adjacency matrix
11.3
Network visualization
11.3.1
Layouts
11.3.2
Node labels
11.3.3
Node shapes and sizes
11.3.4
Edge appearance
References
Rendered with bookdown
Visualization in R workshop
References