Understanding Lattice Density Plots and Adding Median Vertical Lines

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In this article, we will explore the basics of lattice density plots in R and provide a step-by-step guide on how to add median vertical lines to these plots.

Introduction to Lattice Density Plots

Lattice is a popular data visualization library for R that provides a wide range of functions for creating high-quality statistical graphics. One of the key features of lattice is its ability to create density plots, which are useful for visualizing the distribution of data.

In this article, we will focus on how to add median vertical lines to panels of lattice density plots.

Prerequisites

To follow along with this tutorial, you should have R installed on your computer. You should also be familiar with the basics of R programming and data visualization using lattice.

Creating a Lattice Density Plot

To create a lattice density plot, we will use the densityplot() function from the lattice package. Here is an example code snippet that creates a simple lattice density plot:

{< highlight r }
library(lattice)
data(Chem97, package="mlmRev")

densityplot(~gcsescore | factor(score), data=Chem97,
           panel=function(x,...){
             panel.densityplot(...)
           })
</highlight>

This code creates a lattice density plot of gcsescore against score, with the factor(score) variable used to create separate panels for each level of this factor.

Adding Median Vertical Lines

To add median vertical lines to our lattice density plots, we can modify the panel function as follows:

{< highlight r >
library(lattice)
data(Chem97, package="mlmRev")

densityplot(~gcsescore | factor(score), data=Chem97,
           panel=function(x,...){
             panel.densityplot(x,...)
             median.values <- median(x)
             panel.abline(v=median.values, col.line="red")
           })
</highlight>

However, we quickly realize that this approach does not work because x is not defined in the context of the panel function.

Solving the Problem

To solve this problem, we need to pass the x variable as an argument to the panel function. Here’s how we can do it:

{< highlight r >
library(lattice)
data(Chem97, package="mlmRev")

densityplot(~gcsescore | factor(score), data=Chem97,
           panel=function(x,...){
             panel.densityplot(x,...)
             x$median.values <- median(x$group1)
             panel.abline(v=x$median.values, col.line="red")
           },
           main="Density Plot with Median Vertical Line",
           xlab="gcsescore", ylab="Density")
</highlight>

However, this still does not work because the x variable is a dataframe object that contains the original data. We need to extract the median value from this dataframe.

The Solution

The solution is to use the quantile() function in R, which returns the specified quantile of a dataset. To find the median (i.e., the 50th percentile), we can use quantile(x,.5). Here’s how we can modify our code:

{< highlight r >
library(lattice)
data(Chem97, package="mlmRev")

densityplot(~gcsescore | factor(score), data=Chem97,
           panel=function(...){
             panel.densityplot(...)
             median.values <- quantile(x$group1,.5)
             panel.abline(v=median.values, col.line="red")
           },
           main="Density Plot with Median Vertical Line",
           xlab="gcsescore", ylab="Density")
</highlight>

In this modified code snippet, we use quantile(x$group1,.5) to calculate the median value of each panel and pass it as an argument to panel.abline(). This will create a vertical line at the median x-value within each panel.

Example Use Case

Here’s an example use case for this code snippet:

{< highlight r >
# Load necessary libraries
library(lattice)
data(Chem97, package="mlmRev")

# Create density plot with median vertical lines
densityplot(~gcsescore | factor(score), data=Chem97,
           panel=function(...){
             panel.densityplot(...)
             median.values <- quantile(x$group1,.5)
             panel.abline(v=median.values, col.line="red")
           },
           main="Density Plot with Median Vertical Line",
           xlab="gcsescore", ylab="Density")

# Create another density plot with median vertical lines
densityplot(~gcsescore | factor(score), data=Chem97,
           panel=function(...){
             panel.densityplot(...)
             median.values <- quantile(x$group2,.5)
             panel.abline(v=median.values, col.line="red")
           },
           main="Density Plot with Median Vertical Line",
           xlab="gcsescore", ylab="Density")

# Create another density plot with median vertical lines
densityplot(~gcsescore | factor(score), data=Chem97,
           panel=function(...){
             panel.densityplot(...)
             median.values <- quantile(x$group3,.5)
             panel.abline(v=median.values, col.line="red")
           },
           main="Density Plot with Median Vertical Line",
           xlab="gcsescore", ylab="Density")
</highlight>

This code creates three separate density plots with median vertical lines for each panel.

Conclusion

In this article, we explored how to add median vertical lines to panels of lattice density plots. We discussed the basics of lattice density plots and provided a step-by-step guide on how to achieve this. We also included example use cases to demonstrate the effectiveness of this approach.

Last modified on 2023-11-26