How to represent subclusters within clusters on variables with a line graph in R

Question

I want to represent subclusters within clusters on variables using line graphs. I am using R.

I have two categorical variables (clusters; denoted below as a,b,c) which are nested such that each cluster has multiple subclusters (a1, a2, a3, b1, b2 and so on) within it.

I also have multiple numeric variables which I want to display by cluster and subcluster. I would like to use line graphs to display the means of the numeric variables. I have succeeded in displaying the means using summarize(),melt(), and ggplot with facet_wrap to separate the clusters. However, I don't know how I could display the subclusters.

I want to display the cluster means in with a thick black line, while displaying the subcluster means on the same graph, but "greyed out" and thinner to de-emphasize them. I have successfully used facet_wrap to separate the clusters, but I cannot think of how to get the subcluster means on the same graph.

I generated this dataset to illustrate the issue:

library(reshape)
library(tidyverse)

cases <- c(1:27)
cluster1 <- sort(rep(c("a","b","c"),9))
cluster2 <- sort(rep(c("a1","a2","a3","b1","b2","b3","c1","c2","c3"),3))

v1 <- runif(27,min = -2, max = 2)
v2 <- runif(27,min = -3, max = 1)
v3 <- runif(27,min = -4, max = 0)

df <- data.frame(cases,cluster1,cluster2,v1,v2,v3)

means.df <- subset(df) %>%
  group_by(cluster1)%>%
  summarise_at(vars(c(3:5)),mean)
means.df <- as.data.frame(means.df)

melt.df <- melt(means.df,id ="cluster1")

ggplot(data = melt.df,aes(x = variable, y = value, group = cluster1))+
  geom_line()+
  geom_point()+
  ylab("Mean")+
  theme(axis.text.x = element_text(angle = 90,hjust = 1,vjust=0.3))+
  facet_wrap(facets="cluster1")

Thank you in advance. Please let me know if I can provide more details.

Answer 1

You can use a different data origin to plot different layers of data as in geom_line(data = plotU, ...)

df <- data.frame(cases,cluster1,cluster2,v1,v2,v3) |>
  pivot_longer(cols = starts_with("v"), names_to = "variable")

plotD <- df |>
  group_by(variable, cluster1, cluster2) |>
  summarize(value = mean(value), .groups = "drop")

plotU <- df |>
  group_by(variable, cluster1) |>
  summarize(value = mean(value), .groups= "drop")

ggplot(plotD, aes(x = variable, y = value)) +
  geom_line(aes(group = cluster2), alpha = 0.5, lty = 2) +
  geom_line(data = plotU, color = "black", group = "cluster1", size = 1.4) +
  ylab("Mean")+
  theme(axis.text.x = element_text(angle = 90,hjust = 1,vjust=0.3))+
  facet_wrap(facets="cluster1")