dplyr & tidyverse for data processing

Overview

Questions:
  • How can I load tabular data into R?

  • How can I slice and dice the data to ask questions?

Objectives:
  • Read data with the built-in read.csv

  • Read data with dplyr’s read_csv

  • Use dplyr and tidyverse functions to cleanup data.

Requirements:
Time estimation: 1 hour
Level: Advanced Advanced
Supporting Materials:
Last modification: Oct 20, 2021
License: Tutorial Content is licensed under MIT The GTN Framework is licensed under MIT

Best viewed in a Jupyter Notebook

This tutorial is best viewed in a Jupyter notebook! You can load this notebook in Jupyter on one of the UseGalaxy.* servers

Launching the notebook in Jupyter in Galaxy

  1. Instructions to Launch JupyterLab
  2. Open a Terminal in JupyterLab with File -> New -> Terminal
  3. Run wget https://training.galaxyproject.org/archive/2021-12-01/topics/data-science/tutorials/r-dplyr/tutorial.md.ipynb
  4. Select the notebook that appears in the list of files on the left.

Downloading the notebook

  1. Right click this link: tutorial.ipynb
  2. Save Link As..

dplyr is a powerful R-package to transform and summarize tabular data with rows and columns. For further exploration please see the dplyr package vignette: Introduction to dplyr

comment Comment

This tutorial is significantly based on GenomicsClass/labs.

Agenda

In this tutorial, we will cover:

  1. Why Is It Useful?
  2. How Does It Compare To Using Base Functions R?
  3. How Do I Get dplyr?
  4. Data: Mammals Sleep
  5. Important dplyr Verbs To Remember
  6. dplyr Verbs In Action
    1. Pipe Operator: %>%
    2. Selecting Columns Using select()
    3. Selecting Rows Using filter()
    4. Arrange Or Re-order Rows Using arrange()
    5. Create New Columns Using mutate()
    6. Create summaries of the tibble using summarise()
    7. Group operations using group_by()
    8. ggplot2

Why Is It Useful?

The package contains a set of functions (or “verbs”) that perform common data manipulation operations such as filtering for rows, selecting specific columns, re-ordering rows, adding new columns and summarizing data.

In addition, dplyr contains a useful function to perform another common task which is the “split-apply-combine” concept. We will discuss that in a little bit.

How Does It Compare To Using Base Functions R?

If you are familiar with R, you are probably familiar with base R functions such as split(), subset(), apply(), sapply(), lapply(), tapply() and aggregate(). Compared to base functions in R, the functions in dplyr are easier to work with, are more consistent in the syntax and are targeted for data analysis around tibbles, instead of just vectors.

How Do I Get dplyr?

To install and load the required packages:

install.packages(c("dplyr", "readr"))
library(dplyr) # This provides data processing functions
library(readr) # This provides the `read_csv` function

Data: Mammals Sleep

The msleep (mammals sleep) data set contains the sleep times and weights for a set of mammals. This data set contains 83 rows and 11 variables.

url <- "https://raw.githubusercontent.com/genomicsclass/dagdata/master/inst/extdata/msleep_ggplot2.csv"
msleep <- read_csv(url)
head(msleep)

The columns (in order) correspond to the following:

column name Description
name common name
genus taxonomic rank
vore carnivore, omnivore or herbivore?
order taxonomic rank
conservation the conservation status of the mammal
sleep_total total amount of sleep, in hours
sleep_rem rem sleep, in hours
sleep_cycle length of sleep cycle, in hours
awake amount of time spent awake, in hours
brainwt brain weight in kilograms
bodywt body weight in kilograms

Compare the above output with the more traditional read.csv that is built into R

dfmsleep <- read.csv(url)
head(dfmsleep)

This is a “data frame” and was the basis of data processing for years in R, and is still quite commonly used! But notice how dplyr has a much prettier and more consice output. This is what is called a tibble (like a table). We can immediately see metadata about the table, the separator that was guessed for us, what datatypes each column was (dbl or chr), how many rows and columns we have, etc. The tibble works basically exactly like a data frame except it has a lot of features to integrate nicely with the dplyr package.

That said, all of the functions below you will learn about work equally well with data frames and tibbles, but tibbles will save you from filling your screen with hundreds of rows by automatically truncating large tables unless you specifically request otherwise.

Important dplyr Verbs To Remember

dplyr verbs Description SQL Equivalent Operation
select() select columns SELECT
filter() filter rows WHERE
arrange() re-order or arrange rows ORDER BY
mutate() create new columns SELECT x, x*2 ...
summarise() summarise values n/a
group_by() allows for group operations in the “split-apply-combine” concept GROUP BY

dplyr Verbs In Action

The two most basic functions are select() and filter(), which selects columns and filters rows respectively.

Pipe Operator: %>%

Before we go any further, let’s introduce the pipe operator: %>%. dplyr imports this operator from another package (magrittr).This operator allows you to pipe the output from one function to the input of another function. Instead of nesting functions (reading from the inside to the outside), the idea of piping is to read the functions from left to right. This is a lot more like how you would write a bash data processing pipeline and can be a lot more readable and intuitive than the nested version.

Here’s is the more old fashioned way of writing the equivalent code:

head(select(msleep, name, sleep_total))

Now in this case, we will pipe the msleep tibble to the function that will select two columns (name and sleep_total) and then pipe the new tibble to the function head(), which will return the head of the new tibble.

msleep %>% select(name, sleep_total) %>% head(2)

Selecting Columns Using select()

Select a set of columns: the name and the sleep_total columns.

msleep %>% select(name, sleep_total)

To select all the columns except a specific column, use the “-“ (subtraction) operator (also known as negative indexing):

msleep %>% select(-name)

To select a range of columns by name, use the “:” (colon) operator:

msleep %>% select(name:order)

To select all columns that start with the character string “sl”, use the function starts_with():

msleep %>% select(starts_with("sl"))

Some additional options to select columns based on a specific criteria include:

Function Usage
ends_with() Select columns that end with a character string
contains() Select columns that contain a character string
matches() Select columns that match a regular expression
one_of() Select column names that are from a group of names

Selecting Rows Using filter()

Filter the rows for mammals that sleep a total of more than 16 hours.

msleep %>% filter(sleep_total >= 16)

Filter the rows for mammals that sleep a total of more than 16 hours and have a body weight of greater than 1 kilogram.

msleep %>% filter(sleep_total >= 16, bodywt >= 1)

Filter the rows for mammals in the Perissodactyla and Primates taxonomic order

msleep %>% filter(order %in% c("Perissodactyla", "Primates"))

You can use the boolean operators (e.g. >, <, >=, <=, !=, %in%) to create the logical tests.

Arrange Or Re-order Rows Using arrange()

To arrange (or re-order) rows by a particular column, such as the taxonomic order, list the name of the column you want to arrange the rows by:

msleep %>% arrange(order) %>% select(order, genus, name)

Now we will select three columns from msleep, arrange the rows by the taxonomic order and then arrange the rows by sleep_total. Finally, show the final tibble:

msleep %>%
    select(name, order, sleep_total) %>%
    arrange(order, sleep_total)

Same as above, except here we filter the rows for mammals that sleep for 16 or more hours, instead of showing the whole tibble:

msleep %>%
    select(name, order, sleep_total) %>%
    arrange(order, sleep_total) %>%
    filter(sleep_total >= 16)

Something slightly more complicated: same as above, except arrange the rows in the sleep_total column in a descending order. For this, use the function desc()

msleep %>%
    select(name, order, sleep_total) %>%
    arrange(order, desc(sleep_total)) %>%
    filter(sleep_total >= 16)

Create New Columns Using mutate()

The mutate() function will add new columns to the tibble. Create a new column called rem_proportion, which is the ratio of rem sleep to total amount of sleep.

msleep %>%
  mutate(rem_proportion = sleep_rem / sleep_total) %>%
  select(starts_with("sl"), rem_proportion)

You can many new columns using mutate (separated by commas). Here we add a second column called bodywt_grams which is the bodywt column in grams.

msleep %>%
    mutate(rem_proportion = sleep_rem / sleep_total,
           bodywt_grams = bodywt * 1000) %>%
    select(sleep_total, sleep_rem, rem_proportion, bodywt, bodywt_grams)

Create summaries of the tibble using summarise()

The summarise() function will create summary statistics for a given column in the tibble such as finding the mean. For example, to compute the average number of hours of sleep, apply the mean() function to the column sleep_total and call the summary value avg_sleep.

msleep %>%
    summarise(avg_sleep = mean(sleep_total))

There are many other summary statistics you could consider such sd(), min(), max(), median(), sum(), n() (returns the length of vector), first() (returns first value in vector), last() (returns last value in vector) and n_distinct() (number of distinct values in vector).

msleep %>%
    summarise(avg_sleep = mean(sleep_total),
              min_sleep = min(sleep_total),
              max_sleep = max(sleep_total),
              total = n())

Group operations using group_by()

The group_by() verb is an important function in dplyr. As we mentioned before it’s related to concept of “split-apply-combine”. We literally want to split the tibble by some variable (e.g. taxonomic order), apply a function to the individual tibbles and then combine the output.

Let’s do that: split the msleep tibble by the taxonomic order, then ask for the same summary statistics as above. We expect a set of summary statistics for each taxonomic order.

msleep %>%
    group_by(order) %>%
    summarise(avg_sleep = mean(sleep_total),
              min_sleep = min(sleep_total),
              max_sleep = max(sleep_total),
              total = n())

ggplot2

Most people want to slice and dice their data before plotting, so let’s demonstrate that quickly by plotting our last dataset

msleep %>%
    group_by(order) %>%
    summarise(avg_sleep = mean(sleep_total),
              min_sleep = min(sleep_total),
              max_sleep = max(sleep_total),
              total = n()) %>%
    ggplot() + geom_point(aes(x=min_sleep, y=max_sleep, colour=order))

Notice how we can just keep piping our data together, this makes it incredibly easier to experiment and play around with our data and test out what filtering or summarisation we want and how that will plot in the end. If we wanted, or if the data processing is an especially computationally expensive step, we could save it to an intermediate variable before playing around with plotting options, but in the case of this small dataset that’s probably not necessary.

Key points

  • Dplyr and tidyverse make it a lot easier to process data

  • The functions for selecting data are a lot easier to understand than R’s built in alternatives.

Frequently Asked Questions

Have questions about this tutorial? Check out the FAQ page for the Foundations of Data Science topic to see if your question is listed there. If not, please ask your question on the GTN Gitter Channel or the Galaxy Help Forum

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Citing this Tutorial

  1. Helena Rasche, 2021 dplyr & tidyverse for data processing (Galaxy Training Materials). https://training.galaxyproject.org/archive/2021-12-01/topics/data-science/tutorials/r-dplyr/tutorial.html Online; accessed TODAY
  2. Batut et al., 2018 Community-Driven Data Analysis Training for Biology Cell Systems 10.1016/j.cels.2018.05.012

details BibTeX

@misc{data-science-r-dplyr,
author = "Helena Rasche",
title = "dplyr & tidyverse for data processing (Galaxy Training Materials)",
year = "2021",
month = "10",
day = "20"
url = "\url{https://training.galaxyproject.org/archive/2021-12-01/topics/data-science/tutorials/r-dplyr/tutorial.html}",
note = "[Online; accessed TODAY]"
}
@article{Batut_2018,
    doi = {10.1016/j.cels.2018.05.012},
    url = {https://doi.org/10.1016%2Fj.cels.2018.05.012},
    year = 2018,
    month = {jun},
    publisher = {Elsevier {BV}},
    volume = {6},
    number = {6},
    pages = {752--758.e1},
    author = {B{\'{e}}r{\'{e}}nice Batut and Saskia Hiltemann and Andrea Bagnacani and Dannon Baker and Vivek Bhardwaj and Clemens Blank and Anthony Bretaudeau and Loraine Brillet-Gu{\'{e}}guen and Martin {\v{C}}ech and John Chilton and Dave Clements and Olivia Doppelt-Azeroual and Anika Erxleben and Mallory Ann Freeberg and Simon Gladman and Youri Hoogstrate and Hans-Rudolf Hotz and Torsten Houwaart and Pratik Jagtap and Delphine Larivi{\`{e}}re and Gildas Le Corguill{\'{e}} and Thomas Manke and Fabien Mareuil and Fidel Ram{\'{\i}}rez and Devon Ryan and Florian Christoph Sigloch and Nicola Soranzo and Joachim Wolff and Pavankumar Videm and Markus Wolfien and Aisanjiang Wubuli and Dilmurat Yusuf and James Taylor and Rolf Backofen and Anton Nekrutenko and Björn Grüning},
    title = {Community-Driven Data Analysis Training for Biology},
    journal = {Cell Systems}
}
                

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