Plotting1.md

Publication-quality graphics

author: date: autosize: true

Intro

• This is a big topic!
• We are only covering programmable graphics, namely those that can be made directly from data files.

Writing

• Success in science means being a professional writer.
• A key part of this is effective visualization of results.
• This is time-consuming work.

Putting papers together

• Write Methods to break writer's block
• Make figures
• Write about the figures
• Write Discussion, Intro, Abstract
• Reread it all and write title

History of plotting in R

• Base R lets you do pretty much anything, but it can be quite hard.
• grid and gridExtra came along to make various layout tasks easier
• lattice came along to allow "trellis" plots
• ggplot2 tries to simplify the grammar, unify previous disparate concepts, in order to let you do EDA faster.

Setup

library(ggplot2)
library(datasets)
head(mtcars)

                   mpg cyl disp  hp drat    wt  qsec vs am gear carb
Mazda RX4         21.0   6  160 110 3.90 2.620 16.46  0  1    4    4
Mazda RX4 Wag     21.0   6  160 110 3.90 2.875 17.02  0  1    4    4
Datsun 710        22.8   4  108  93 3.85 2.320 18.61  1  1    4    1
Hornet 4 Drive    21.4   6  258 110 3.08 3.215 19.44  1  0    3    1
Hornet Sportabout 18.7   8  360 175 3.15 3.440 17.02  0  0    3    2
Valiant           18.1   6  225 105 2.76 3.460 20.22  1  0    3    1

Let's list what is wrong with this plot

Let's list what is wrong with this plot

Colors

• Avoid plots that color-blind people cannot see
• Use shapes, line types, etc.
• [here](http://www.cookbook-r.com/Graphs/Colors_(ggplot2\))
• viridis is something you should know!

Resources

• color blindness simulator
• Fundamentals of Data Visualization, which will be published by O'Reilly soon. The author is and evolutionary biologist and chair of Integrative Biology at UT Austin.