1. Next Generation R tidyr, dplyr, ggplot2
R-based advanced methods for deep sequencing analysis
Weizmann Institute of Science, 2017
Gil Hornung
Bioinformatics Analyst, G-INCPM, Weizmann

2. The “tidyverse”
Make data manipulation and visualization easier to write and read – by data scientists for data scientists.
Set of self-consistent packages (tidyr, dplyr, ggplot2, tibble, purrr, readr, lubridate…).
Open source, but mainly developed and maintained by Hadley Wickham.

3. Talk outline Data manipulation: Preliminary concepts:
Tidy data
Pipe
Examples (the best!)
Data visualization:
Preliminary concept – Grammar of graphics
Examples

4. (Un)tidy data Same data, different representations: Patient Year 1
Jon Snow
119/76
116/79
122/81
Theon Greyjoy
116/75
120/81
166/87
Eddard Stark
118/78 NA
Patient
Jon Snow
Theon Greyjoy
Eddard Stark
Year 1
119/76
120/75
118/78
Year 2
116/79
125/81 NA
Year 3
122/80
166/87
Patient
Systolic
Diastolic
Jon Snow
119,116,122
76,79,81
Theon Greyjoy
116,120,166
75,81,87
Eddard Stark
118,NA,NA
78,NA,NA

5. Tidy data Each row is identifiable by a combination of “key” columns
Values of observations appear in columns
Patient
Year
Systolic
Diastolic
Jon Snow 1
120 80 2
125 83 3
122
Theon Greyjoy 75 81
166 87
Eddard Stark
118 78
Each observation forms a row

6. Tidy data Easy to add new observations Patient Year Systolic Diastolic
Age
House
Jon Snow 1
120 80 16
Stark 2
125 83 17 3
122 18
Theon Greyjoy 75
Greyjoy 81
166 87 19
Eddard Stark
118 78 35
Easy to add new observations

7. Talk outline Data manipulation: Preliminary concepts:
Tidy data
Pipe
Examples (the best!)
Data visualization:
Preliminary concept – Grammar of graphics
Examples

8. Pipe
Simple connection between output of one function to the input of the next function.
Instead of:
> round(scale(abs(log2(x)),center = T,scale = F),2)
Use a pipe:
> x %>%
log2 %>%
abs %>%
scale(.,center=T,scale=F) %>%
round(.,2)
Pipe operator
Rstudio shortcut:
Ctrl+shift+m
A do to represent where the output should be used as input

9. Talk outline Data manipulation: Preliminary concepts:
Tidy data
Pipe
Examples (the best!)
Data visualization:
Preliminary concept – Grammar of graphics
Examples

11. Joins A B A %>% inner_join(B) A %>% left_join(B) A %>%
right_join(B)
A %>%
full_join(B)

12. “Not really” joins A B A %>% semi_join(B) A %>% anti_join(B)
“intersect” values of keys
“subtract” values of keys

13. tidyr example 2 - MSigDB gene set format
Hint:
extract() can get multiple values:
"(.*?)\t(.*?)”

14. Talk outline Data manipulation: Preliminary concepts:
Tidy data
Pipe
Examples (the best!)
Data visualization:
Preliminary concept – Grammar of graphics
Examples

15. Grammar of graphics
Established philosophy (Wilkinson, 2005) behind ggplot2.
Decomposes a plot to the following main components:
Component
ggplot2 syntax
Description
Data
A tidy data frame
Aesthetic mapping
aes()
Mapping of variables to aesthetic attributes (e.g. which column is the x position? which column is the color?)
Geometries
geom_
The geometric shapes that will represent the data (e.g. bar, line, points…)
More components: scale_, stat_, coord_, facet_, theme
Layers – add data, then geom, then another geom then stat / facet etc.

16. Grammar of graphics ggplot(data=mpg, aes(x=hwy, y=cty)) + geom_point()
Data frame
Aesthetics mapping from column to position
Geometric elements to use

18. Talk outline Data manipulation: Preliminary concepts:
Tidy data
Pipe
Examples (the best!)
Data visualization:
Preliminary concept – Grammar of graphics
Examples

19. ggplot2 example 1 – Expression of a single gene
PRJEB18261: RNA-seq of A431 cell line after gefitinib treatment

20. ggplot2 example 2 – Somatic mutation rates
MS Lawrence et al. (2013) doi: /nature12213

21. ggplot2 example 2 – Somatic mutation rates

22. Next Generation R knitr
R-based advanced methods for deep sequencing analysis
Weizmann Institute of Science, 2017
Gil Hornung
Bioinformatics Analyst, G-INCPM, Weizmann

23. knitr
Dynamic report generation – R code is evaluated during the generation of the report.
Based on markdown – a markup language that is easy-to-read and easy-to-write plain text format.
Supports output as HTML, PDF…
Open source, but mainly developed and maintained by Yihui Xie.

24. knitr