ggplot2 two

BIOS 611: Introduction to Data Science

Instructor Matt Biggs

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Overview of today

• Logistics:
• First homework due by the end of next class
• Review last class materials on ggplot
• ggplot continued—plotting in R

BIOS 611

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Review

• Aesthetics:
• ggplot(dataset, aes(x=col1, y=col2)) # set global figure properties
• + geom_point(aes(size=col3)) # set layer-specific properties
• Assigning colors manually:
• Answer: scale_manual_fill(), scale_manual_color()
• Example

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BIOS 611

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Objectives

• Students will understand more ggplot syntax and be able to produce more advanced plots
• Students will be familiar with R markdown (Rmd)

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BIOS 611

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More Syntax of ggplot

Lines and groups

Annotations

Axis limits

Expressions in labels

Themes

Legends

Hex colors

scripts/intro2ggplot2.R

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BIOS 611

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R markdown

Markdown is a simple, plain-text syntax for formatting text and document layouts.

For example (here’s a cheat sheet with many more commands):

*italics*, **bold**, # Header1, ## Header 2, * Bulleted list


[text](hyperlink)

scripts/intro2rmd.Rmd

BIOS 611

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GitHub markdown

There are lots of versions of Markdown. They’re all similar, with small variations in syntax.

For example here’s a GitHub markdown cheat sheet. This is what you use in a README.md in your Git repositories.

Unordered list:

* Item 1

* Item 2

* Item 2a

* Item 2b

BIOS 611

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QUIZ

In-class practice

1. Re-create the figure to the right using Rmd
2. Name the Rmd document “diamond_bin.Rmd” and the knit PDF “diamond_bin.pdf”. Place in a directory called “class_examples” in your course Git repository.
3. Push to GitHub.
4. Hint: Notice that the theme is minimal, italics “G”, the bold “ideal”, the bulleted list, the figure title, the text annotation “G”

BIOS 611

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Homework due next class

1. Re-create the figure to the right using an R script and ggsave()
2. Push the resulting script titled “HW1_your_github_id.R” and image “HW1_your_github_id.png” to Github classroom under a directory called “homework”
3. Hints:
1. Load the “datasets” package and then load the CO₂ data set.
2. Pay attention to the expressions used in the axis labels and title to achieve the subscripts
3. Use geom_smooth with se=FALSE
4. Change the legend title
5. Save with height=3, width=5
4. Submit by midnight on the due date

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BIOS 611

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