Assignment information: (delete this when you submit) In this assignment you will re-build the pie graphs shown in the paper “Genomics is failing on diversity” by Popejoy and Fullerton (https://www.nature.com/articles/538161a). Delete all instructions and replace with short explanatory text about all code chunks. Be sure to change the title in the YAML header.

If possible, save this file to your Teams folder.

Introduction

Write a brief introduction about the data being plotted, including the information

Alice B. Popejoy and Stephanie M. Fullerton collected data on the ethnic backgrounds of participants in all GWAS studies performed upto 2009. This data was taken from 373 GWAS studies in the GWAS catalog. Results of this study showed that almost all participants included in these studies were of European descent. They repeated this study using new data in 2016 because there had been more than a 2000% increase in data collected.

Create data

Create vectors to contain the data and labels to make the pie graphs at the top of figures.

Each vector has 3 elements: European ancestry, Asian ancestry, and other non-European ancestry.

DO NOT name your vector for the labels “labels”, since this is the name of an existing R function.

Include new line characters in the text as needed to improve spacing.

study2009<-c(96, 3, 1)
study2016<-c(81, 14, 5)
labels<-c("European \nancestry","Asian","Other \nnon-European")

Pie graphs

  1. Create a 1 x 2 grid using the command par(mfrow = c(1,2))
  2. Plot the 2009 data on the left and 2016 data on the right.
  3. This will require setting up the pie command twomce
  4. Use the argument main = … to add a title to above the plots
  5. Set the argument init.angle = … to -82. Experiment with how this affects the plot.
  6. Set the argument radius = … to 1. Experiment with how this affects the plot.
  7. Set the argument col = … to c(1,2,3), then experiment with different numbers. Try to make it ugly.
# set up par()
par(mfrow = c(1,2), mar = c(8,2, 8, 2))

#pie graphs 1
# add main, init.angle, radius, and col
pie(study2009, labels, main = 2009, init.angle = -182, radius = 1, col = c(1,2,3))

# pie graph 2
# add main, init.angle, radius, and col
pie(study2016, labels, main = 2016, init.angle = -182, radius = 1, col = c(1,2,3))

Bar graphs

If you want, you can examine this code below to see how stracked bar graphs are made

# data
dat2016 <- c(14, 3,1,0.54,0.28,0.08,0.05)
dat2016_rev <- rev(dat2016)
barplotdata2016 <- matrix(c(dat2016_rev))

# labels
labels_x <- rev(c("Asian","African","Mixed", "Hispanic &\nLatin American",
                        "Pacific Islander","Arab & Middle East","Native peoples"))

par(mfrow = c(1,1))

barplot(barplotdata2016,
        width = 0.01, 
        xlim = c(0,0.1),
         axes = F,
        col = c(1,2,3,4,5,6,7),
        legend.text = labels_x)