Lesson 3 Exercise Questions: Building a Publication Quality Plot

Putting what we have learned to the test:
The following questions synthesize several of the skills you have learned thus far. It may not be immediately apparent how you would go about answering these questions. Remember, the R community is expansive, and there are a number of ways to get help including but not limited to google search. These questions have multiple solutions, but you should try to stick to the tools you have learned to use thus far.

Your mission is to make a publishable figure.

We will use the iris data set for this.

Start by loading ggplot2.

if (!requireNamespace("ggplot2", quietly = TRUE)) install.packages("ggplot2")

library(ggplot2)

Q1. Start by creating a scatter plot of iris with Petal.Length on the x-axis and Petal.Width on the y-axis. Color the points by Species.

ggplot(iris)+
  geom_point(aes(Petal.Length,Petal.Width,color=Species))

Q2. Fix the axes so that the dimensions on the x-axis and the y-axis are equal (See ?coord_fixed). Both axes should start at 0. Label the axis breaks every 0.5 units on the y-axis and every 1.0 units on the x-axis.

ggplot(iris)+
  geom_point(aes(Petal.Length,Petal.Width,color=Species))+
  coord_fixed(ratio=1,ylim=c(0,2.75),xlim=c(0,7)) +
  scale_y_continuous(breaks=seq(0,2.5, by=0.5)) +
  scale_x_continuous(breaks=0:7)

Q3. Assign a color blind friendly palette to the color of the points, and change the legend title to "Iris Species". Label the x and y axes to make the variable names visually appealing; include unit information.

#multiple ways to find color blind friendly palettes. 
#using color brewer scales 
RColorBrewer::display.brewer.all(colorblindFriendly=TRUE)

ggplot(iris)+
  geom_point(aes(Petal.Length,Petal.Width,color=Species))+
  coord_fixed(ratio=1,ylim=c(0,2.75),xlim=c(0,7)) +
  scale_y_continuous(breaks=seq(0,2.5, by=0.5)) +
  scale_x_continuous(breaks=0:7) +
  scale_color_brewer(palette = "Dark2",name="Iris Species") +
  labs(x="Petal Length (cm)", y= "Petal Width (cm)")

Q4. Play with the theme to make your plot nicer and more publishable. Change font style to "Times". Change all font sizes to 12 pt font. Bold the legend title and the axes titles. Increase the size of the points on the plot to 2. Bonus: fill the points with color and have a black outline around each point.

ggplot(iris)+
  geom_point(aes(Petal.Length,Petal.Width,fill=Species),size=2,shape=21)+
  coord_fixed(ratio=1,ylim=c(0,2.75),xlim=c(0,7)) +
  scale_y_continuous(breaks=seq(0,2.5, by=0.5)) +
  scale_x_continuous(breaks=0:7) +
  scale_fill_brewer(palette = "Dark2",name="Iris Species") +
  labs(x="Petal Length (cm)", y= "Petal Width (cm)") +
  theme_bw()+
  theme(axis.text=element_text(family="Times",size=12),
        axis.title=element_text(family="Times",face="bold",size=12),
        legend.text=element_text(family="Times",size=12),
        legend.title = (element_text(family="Times",face="bold",size=12))
        )

Q5. Save your plot using ggsave.

ggsave("iris.tiff", width=5.5, height=3.5,units="in")