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A Guide to Getting Started with R

8 Chapter 8: Pimping Your Plots 

install.packages("ggplot2",  repos = "https://cran.us.r-project.org")
install.packages("dplyr",  repos = "https://cran.us.r-project.org")
install.packages("gridExtra",  repos = "https://cran.us.r-project.org")
urlfile08a="https://raw.githubusercontent.com/apicellap/data/main/compensation.csv"
compensation<-read.csv(url(urlfile08a))
head(compensation)
##    Root Fruit  Grazing
## 1 6.225 59.77 Ungrazed
## 2 6.487 60.98 Ungrazed
## 3 4.919 14.73 Ungrazed
## 4 5.130 19.28 Ungrazed
## 5 5.417 34.25 Ungrazed
## 6 5.359 35.53 Ungrazed

Create base scatterplot:

eg_scatter <- ggplot(compensation, aes(x = Root, y = Fruit)) +
                     geom_point()
eg_scatter

Create base boxplot:

eg_box <- ggplot(compensation, aes(x = Grazing, y = Fruit)) +
  geom_boxplot() 
eg_box

Render blank background:

eg_scatter + theme_bw()

Arrange plots with gridExtra:

grid.arrange(          
  eg_scatter, eg_box,
  nrow =1) #specifies the arrangement

Change axes’ bounds:

eg_scatter +  xlim(0,20) +ylim(0,140)

Add text to plot:

eg_scatter + annotate("text", 
                      x=c(6,8), #6 and 105 are the x,y coordinates for placing the label
                      y=c(105,25),
                      label = c("here","there"))

Modify axis scales:

eg_scatter + 
  scale_x_continuous(limits = c(4,11), #bounds 
                     breaks = 4:11)  #tick marks at 1 step between the bounds 
ggplot(compensation, aes(x = Root, y = Fruit, 
                         color = Grazing)) + #need to add the color to aes for scale_color_manual() to function  
  geom_point() + 
  scale_color_manual(values = c(Grazed = "brown", Ungrazed = "green"))

Transform the scale:

eg_box + scale_y_continuous(breaks = seq(from = 10, to = 150,
                                         by = 20), #vector breakpoints that call for ticks 
                            trans = "log10") #log transformation of y axis

Modifying the theme:

eg_scatter + 
  theme(
    panel.background = element_rect(fill = NA, colour = "black"), #backgrounds is white 
    panel.grid.minor = element_blank(), #no minor gridlines 
    panel.grid.major = element_line(colour = "lightblue") #gridlines are blue 
  )

Modify elements of the x axis:

eg_box + 
  theme(
    axis.title.x = element_text(color = "cornflowerblue",
    size = rel(2)), #relative increase above the default setting 
    axis.text.x = element_text(angle = 45, #angle of x axis labels 
                               size = 13, 
                               vjust =0.5 ) #scoots labels down a bit; can accept values from 0-1
  )

Modify axis labels (categorical variables):

eg_box + 
    scale_x_discrete(limits = c("Ungrazed", "Grazed"), #limits refer to variables in the dataframe
                     labels = c("Control", "Grazed")) #labels() corresponds to the limits and lets you change them without altering the df

Modify legend:

ggplot(compensation, aes(x = Root, y = Fruit, color = Grazing)) + 
  geom_point() + 
  theme(legend.key = element_rect(fill = NA)) #removes box around the legend