GGPlot Stripchart Best Reference - Datanovia (2024)

GGPlot Stripchart

10 mins

Data Visualization using GGPlot2

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Stripcharts are also known as one dimensional scatter plots. These plots are suitable compared to box plots when sample sizes are small.

This article describes how to create and customize Stripcharts using the ggplot2 R package.



Contents:

  • Key R functions
  • Data preparation
  • Loading required R package
  • Basic stripcharts
  • Combine with box plots and violin plots
  • Create a stripchart with multiple groups
  • Conclusion

Related Book

GGPlot2 Essentials for Great Data Visualization in R

Key R functions

  • Key function: geom_jitter()
  • key arguments: color, fill, size, shape. Changes points color, fill, size and shape

Data preparation

  • Demo dataset: ToothGrowth
    • Continuous variable: len (tooth length). Used on y-axis
    • Grouping variable: dose (dose levels of vitamin C: 0.5, 1, and 2 mg/day). Used on x-axis.

First, convert the variable dose from a numeric to a discrete factor variable:

data("ToothGrowth")ToothGrowth$dose <- as.factor(ToothGrowth$dose)head(ToothGrowth, 3)
## len supp dose## 1 4.2 VC 0.5## 2 11.5 VC 0.5## 3 7.3 VC 0.5

Loading required R package

Load the ggplot2 package and set the default theme to theme_classic() with the legend at the top of the plot:

library(ggplot2)theme_set( theme_classic() + theme(legend.position = "top") )

Basic stripcharts

We start by initiating a plot named e, then we’ll add layers. The following R code creates stripcharts combined with summary statistics (mean +/- SD), boxplots and violin plots.

  • Change points shape and color by groups
  • Adjust the degree of jittering: position_jitter(0.2)
  • Add summary statistics:
# Initiate a ggplote <- ggplot(ToothGrowth, aes(x = dose, y = len))# Stripcharts with summary statistics# Change color by dose groupse + geom_jitter(aes(shape = dose, color = dose), position = position_jitter(0.2), size = 1.2) + stat_summary(aes(color = dose), size = 0.4, fun.data="mean_sdl", fun.args = list(mult=1))+ scale_color_manual(values = c("#00AFBB", "#E7B800", "#FC4E07"))

GGPlot Stripchart Best Reference - Datanovia (1)

The function mean_sdl is used for adding mean and standard deviation. It computes the mean plus or minus a constant times the standard deviation. In the R code above, the constant is specified using the argument mult (mult = 1). By default mult = 2. The mean +/- SD can be added as a crossbar or a pointrange.

Combine with box plots and violin plots

# Combine with box plote + geom_boxplot() + geom_jitter(position = position_jitter(0.2)) # Strip chart + violin plot + stat summarye + geom_violin(trim = FALSE) + geom_jitter(position = position_jitter(0.2)) + stat_summary(fun.data="mean_sdl", fun.args = list(mult=1), color = "red")

GGPlot Stripchart Best Reference - Datanovia (2)GGPlot Stripchart Best Reference - Datanovia (3)

Create a stripchart with multiple groups

The R code is similar to what we have seen in dot plots section. However, to create dodged jitter points, you should use the function position_jitterdodge() instead of position_dodge().

e + geom_jitter( aes(shape = supp, color = supp), size = 1.2, position = position_jitterdodge(jitter.width = 0.2, dodge.width = 0.8) ) + stat_summary( aes(color = supp), fun.data="mean_sdl", fun.args = list(mult=1), size = 0.4, position = position_dodge(0.8) )+ scale_color_manual(values = c("#00AFBB", "#E7B800"))

GGPlot Stripchart Best Reference - Datanovia (4)

Conclusion

This article describes how to create a stripchart using the ggplot2 package.



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Course Curriculum

  • Introduction to GGPlot2

    20 mins

  • GGPlot Scatter Plot

    15 mins

  • GGPlot Boxplot

    15 mins

  • GGPlot Violin Plot

    10 mins

  • GGPlot Dot Plot

    15 mins

  • GGPlot Stripchart

    10 mins

  • GGPlot Line Plot

    15 mins

  • GGPlot Barplot

    10 mins

  • GGPlot Error Bars

    15 mins

  • GGPlot Density Plot

    10 mins

  • GGPlot Histogram

    10 mins

  • GGPLOT QQ Plot

    10 mins

  • GGPlot ECDF

    10 mins

  • Combine Multiple GGPlots into a Figure

    15 mins

Teacher

GGPlot Stripchart Best Reference - Datanovia (6)

Alboukadel Kassambara
Role : Founder of Datanovia
  • Website : https://www.datanovia.com/en
  • Experience : >10 years
  • Specialist in : Bioinformatics and Cancer Biology

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GGPlot Stripchart Best Reference - Datanovia (2024)
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