Prepare the data

ToothGrowth data sets are used :

# Convert the variable dose from a numeric to a factor variable ToothGrowth$dose <- as.factor(ToothGrowth$dose) head(ToothGrowth)

## len supp dose ## 1 4.2 VC 0.5 ## 2 11.5 VC 0.5 ## 3 7.3 VC 0.5 ## 4 5.8 VC 0.5 ## 5 6.4 VC 0.5 ## 6 10.0 VC 0.5

Make sure that the variable dose is converted as a factor variable using the above R script.

Basic dot plots

library(ggplot2) # Basic dot plot p<-ggplot(ToothGrowth, aes(x=dose, y=len)) + geom_dotplot(binaxis='y', stackdir='center') p # Change dotsize and stack ratio ggplot(ToothGrowth, aes(x=dose, y=len)) + geom_dotplot(binaxis='y', stackdir='center', stackratio=1.5, dotsize=1.2) # Rotate the dot plot p + coord_flip()

Choose which items to display :

p + scale_x_discrete(limits=c("0.5", "2"))

Add summary statistics on a dot plot

The function stat_summary() can be used to add mean/median points and more to a dot plot.

# dot plot with mean points p + stat_summary(fun.y=mean, geom="point", shape=18, size=3, color="red") # dot plot with median points p + stat_summary(fun.y=median, geom="point", shape=18, size=3, color="red")

# Add basic box plot ggplot(ToothGrowth, aes(x=dose, y=len)) + geom_boxplot()+ geom_dotplot(binaxis='y', stackdir='center') # Add notched box plot ggplot(ToothGrowth, aes(x=dose, y=len)) + geom_boxplot(notch = TRUE)+ geom_dotplot(binaxis='y', stackdir='center') # Add violin plot ggplot(ToothGrowth, aes(x=dose, y=len)) + geom_violin(trim = FALSE)+ geom_dotplot(binaxis='y', stackdir='center')

p <- ggplot(ToothGrowth, aes(x=dose, y=len)) + geom_dotplot(binaxis='y', stackdir='center') p + stat_summary(fun.data="mean_sdl", fun.args = list(mult=1), geom="crossbar", width=0.5) p + stat_summary(fun.data=mean_sdl, fun.args = list(mult=1), geom="pointrange", color="red")

# Function to produce summary statistics (mean and +/- sd) data_summary <- function(x) { m <- mean(x) ymin <- m-sd(x) ymax <- m+sd(x) return(c(y=m,ymin=ymin,ymax=ymax)) }

p + stat_summary(fun.data=data_summary, color="blue")

Change dot plot colors by groups

In the R code below, the fill colors of the dot plot are automatically controlled by the levels of dose :

# Use single fill color ggplot(ToothGrowth, aes(x=dose, y=len)) + geom_dotplot(binaxis='y', stackdir='center', fill="#FFAAD4") # Change dot plot colors by groups p<-ggplot(ToothGrowth, aes(x=dose, y=len, fill=dose)) + geom_dotplot(binaxis='y', stackdir='center') p

It is also possible to change manually dot plot colors using the functions :

• scale_fill_manual() : to use custom colors
• scale_fill_brewer() : to use color palettes from RColorBrewer package
• scale_fill_grey() : to use grey color palettes

# Use custom color palettes p+scale_fill_manual(values=c("#999999", "#E69F00", "#56B4E9")) # Use brewer color palettes p+scale_fill_brewer(palette="Dark2") # Use grey scale p + scale_fill_grey() + theme_classic()

Read more on ggplot2 colors here : ggplot2 colors

Change the legend position

p + theme(legend.position="top") p + theme(legend.position="bottom") p + theme(legend.position="none") # Remove legend

The allowed values for the arguments legend.position are : “left”,“top”, “right”, “bottom”.

Read more on ggplot legends : ggplot2 legend

Change the order of items in the legend

The function scale_x_discrete can be used to change the order of items to “2”, “0.5”, “1” :

p + scale_x_discrete(limits=c("2", "0.5", "1"))

Dot plot with multiple groups

# Change dot plot colors by groups ggplot(ToothGrowth, aes(x=dose, y=len, fill=supp)) + geom_dotplot(binaxis='y', stackdir='center') # Change the position : interval between dot plot of the same group p<-ggplot(ToothGrowth, aes(x=dose, y=len, fill=supp)) + geom_dotplot(binaxis='y', stackdir='center', position=position_dodge(0.8)) p

Change dot plot colors and add box plots :

# Change colors p+scale_fill_manual(values=c("#999999", "#E69F00", "#56B4E9")) # Add box plots ggplot(ToothGrowth, aes(x=dose, y=len, fill=supp)) + geom_boxplot(fill="white")+ geom_dotplot(binaxis='y', stackdir='center') # Change the position ggplot(ToothGrowth, aes(x=dose, y=len, fill=supp)) + geom_boxplot(position=position_dodge(0.8))+ geom_dotplot(binaxis='y', stackdir='center', position=position_dodge(0.8))

Customized dot plots

# Basic dot plot ggplot(ToothGrowth, aes(x=dose, y=len)) + geom_boxplot()+ geom_dotplot(binaxis='y', stackdir='center')+ labs(title="Plot of length by dose",x="Dose (mg)", y = "Length")+ theme_classic() # Change color by groups dp <-ggplot(ToothGrowth, aes(x=dose, y=len, fill=dose)) + geom_dotplot(binaxis='y', stackdir='center')+ labs(title="Plot of length by dose",x="Dose (mg)", y = "Length") dp + theme_classic()

Change fill colors manually :

# Continuous colors dp + scale_fill_brewer(palette="Blues") + theme_classic() # Discrete colors dp + scale_fill_brewer(palette="Dark2") + theme_minimal() # Gradient colors dp + scale_fill_brewer(palette="RdBu") + theme_minimal()

Read more on ggplot2 colors here : ggplot2 colors

Infos

This analysis has been performed using R software (ver. 3.2.4) and ggplot2 (ver. 2.1.0)

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