ggplot2 stripchart (jitter) : Quick start guide - R software and data visualization - Easy Guides - Wiki (2024)

• Prepare the data
• Basic stripcharts
• Add summary statistics on a stripchart
  • Add mean and median points
  • Stripchart with box blot and violin plot
  • Add mean and standard deviation
• Change point shapes by groups
• Change stripchart colors by groups
• Change the legend position
• Change the order of items in the legend
• Stripchart with multiple groups
• Customized stripcharts
• Infos

ToothGrowth data sets are used :

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

library(ggplot2)# Basic stripchartggplot(ToothGrowth, aes(x=dose, y=len)) + geom_jitter()# Change the position# 0.2 : degree of jitter in x directionp<-ggplot(ToothGrowth, aes(x=dose, y=len)) + geom_jitter(position=position_jitter(0.2))p# Rotate the stripchartp + coord_flip()

Choose which items to display :

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

Change point shapes and size :

# Change point sizeggplot(ToothGrowth, aes(x=dose, y=len)) + geom_jitter(position=position_jitter(0.2), cex=1.2)# Change shapeggplot(ToothGrowth, aes(x=dose, y=len)) + geom_jitter(position=position_jitter(0.2), shape=17)

Read more on point shapes : ggplot2 point shapes

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

# stripchart with mean pointsp + stat_summary(fun.y=mean, geom="point", shape=18, size=3, color="red")# stripchart with median pointsp + stat_summary(fun.y=median, geom="point", shape=18, size=3, color="red")

# Add basic box plotggplot(ToothGrowth, aes(x=dose, y=len)) + geom_boxplot()+ geom_jitter(position=position_jitter(0.2))# Add notched box plotggplot(ToothGrowth, aes(x=dose, y=len)) + geom_boxplot(notch = TRUE)+ geom_jitter(position=position_jitter(0.2))# Add violin plotggplot(ToothGrowth, aes(x=dose, y=len)) + geom_violin(trim = FALSE)+ geom_jitter(position=position_jitter(0.2))

p <- ggplot(ToothGrowth, aes(x=dose, y=len)) + geom_jitter(position=position_jitter(0.2))p + stat_summary(fun.data="mean_sdl", mult=1, geom="crossbar", width=0.5)p + stat_summary(fun.data=mean_sdl, 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")

In the R code below, point shapes are controlled automatically by the variable dose.

You can also set point shapes manually using the function scale_shape_manual()

# Change point shapes by groupsp<-ggplot(ToothGrowth, aes(x=dose, y=len, shape=dose)) + geom_jitter(position=position_jitter(0.2))p# Change point shapes manuallyp + scale_shape_manual(values=c(1,17,19))

Read more on point shapes : ggplot2 point shapes

In the R code below, point colors of the stripchart are automatically controlled by the levels of dose :

# Use single colorggplot(ToothGrowth, aes(x=dose, y=len)) + geom_jitter(position=position_jitter(0.2), color="red")# Change stripchart colors by groupsp<-ggplot(ToothGrowth, aes(x=dose, y=len, color=dose)) + geom_jitter(position=position_jitter(0.2))p

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

• scale_color_manual() : to use custom colors
• scale_color_brewer() : to use color palettes from RColorBrewer package
• scale_color_grey() : to use grey color palettes

# Use custom color palettesp+scale_color_manual(values=c("#999999", "#E69F00", "#56B4E9"))# Use brewer color palettesp+scale_color_brewer(palette="Dark2")# Use grey scalep + scale_color_grey() + theme_classic()

Read more on ggplot2 colors here : ggplot2 colors

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

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"))

# Change stripchart colors by groupsggplot(ToothGrowth, aes(x=dose, y=len, color=supp)) + geom_jitter(position=position_jitter(0.2))# Change the position : interval between stripchart of the same groupp<-ggplot(ToothGrowth, aes(x=dose, y=len, color=supp, shape=supp)) + geom_jitter(position=position_dodge(0.8))p

Change stripchart colors and add box plots :

# Change colorsp+scale_color_manual(values=c("#999999", "#E69F00", "#56B4E9"))# Add box plotsggplot(ToothGrowth, aes(x=dose, y=len, color=supp)) + geom_boxplot(color="black")+ geom_jitter(position=position_jitter(0.2))# Change the positionggplot(ToothGrowth, aes(x=dose, y=len, color=supp)) + geom_boxplot(position=position_dodge(0.8))+ geom_jitter(position=position_dodge(0.8))

# Basic stripchartggplot(ToothGrowth, aes(x=dose, y=len)) + geom_boxplot()+ geom_jitter(position=position_jitter(0.2))+ labs(title="Plot of length by dose",x="Dose (mg)", y = "Length")+ theme_classic()# Change color/shape by groupsp <- ggplot(ToothGrowth, aes(x=dose, y=len, color=dose, shape=dose)) + geom_jitter(position=position_jitter(0.2))+ labs(title="Plot of length by dose",x="Dose (mg)", y = "Length")p + theme_classic()

Change colors manually :

# Continuous colorsp + scale_color_brewer(palette="Blues") + theme_classic()# Discrete colorsp + scale_color_brewer(palette="Dark2") + theme_minimal()# Gradient colorsp + scale_color_brewer(palette="RdBu")

Read more on ggplot2 colors here : ggplot2 colors

This analysis has been performed using R software (ver. 3.1.2) and ggplot2 (ver. 1.0.0)