cheatsheet.R

# Simple plot example for geom_point
data(iris)
# where we specify the type of plot with geom_point()
# the data to plot with aes
IrisPlot <- ggplot(iris, aes(Sepal.Length, Petal.Length, colour=Species))+geom_point()
# if we want to change the colour
IrisPlot <- ggplot(iris, aes(Sepal.Length, Petal.Length))+geom_point(colour="blue")
print(IrisPlot)
# Now, let's modify the axes labels and also add title
print(IrisPlot + labs(y="Petal length (cm)", x = "Sepal length (cm)")) + ggtitle("Petal and sepal length of iris")

# Center the title (which is left-aligned by default)
print(IrisPlot + labs(y="Petal length (cm)", x = "Sepal length (cm)")) + ggtitle("Petal and sepal length of iris") + theme(plot.title = element_text(hjust = 0.5))

# Change the title aesthetics
ggplot(pdata, aes(tm, colour=tot_readsbins)) + geom_freqpoly(binwidth = 5) + ggtitle("Tm (by depth)")  + theme(plot.title = element_text(size=40, face = "bold"))


# Example for geom_smooth : for drawing smoothed lines (e.g., for simple trends or approximations)
ggplot(mpg, aes(x = displ, y = hwy)) + geom_smooth()

# Using 2 different geometries in the same plot
ggplot(mpg, aes(x = displ, y = hwy)) + geom_point() + geom_smooth()

# Save to pdf plot
library("ggplot2")
pdf("myplot.pdf")
myplot <- ggplot(mtcars, aes(wt, mpg)) + geom_point()
print(myplot)
dev.off()

# Save to png plot
library("ggplot2")
png("myplot.png") # changing figure size png("plot.png", width=480, height=240, res=120)
myplot <- ggplot(mtcars, aes(wt, mpg)) + geom_point()
print(myplot)
dev.off()

# to save a plot that you have opened use
ggsave("plot.pdf") # if you want to know the size of the plot that will be saved use dev.size()

### creating a multipage pdf
#specify path to save PDF to
destination = 'pdf_ex.pdf'

#open PDF
pdf(file=destination)

#save plots to PDF
for (i in 1:4) {   
  x=rnorm(i)  
  y=rnorm(i)  
  plot(x, y)   
}

#turn off PDF plotting
dev.off() 

# colour pallete , useful when you want to use several colours in a gradient
ggplot(data, aes(x, y,                             # colour_brewer & fill_brewer
                 col = factor(x),
                 fill = factor(x))) + 
  geom_bar(stat = "identity", size = 2) + 
  scale_colour_brewer(palette = "YlOrRd", direction = - 1) + 
  scale_fill_brewer(palette = "BuPu")
  
# if, instead of using a predefined pallete, we want to use the customised colours we need to do:
p <- ggplot(mtcars, aes(mpg, wt)) +
  geom_point(aes(colour = factor(cyl)))
p + scale_colour_manual(values = c("red", "blue", "green"))