How to plot cluster of binary variables in R?

Question

Hi!

I'm new to using kmeans and clustering in R. I've been trying to figure out how to visualize the clusters in a pretty and presentable way.

I've attached a table of what the data looks like. There are more column variables but this sample should do. This data is originally from a survey and answers were recorded as 0s and 1s and then clustered using kmeans accordingly.

I'd appreciate any advice or help on how to plot this.

Answer 1

I think the easiest way to do this would be by some type of ordination, and then plotting the ordination with the text labels indicating which cluster a data point is in.

I will give an example using data included in the vegan program. I will not include steps like standardizing data before the ordination or indicate what ordination method should be used. That will vary depending on the type of data.

library(vegan)
data(varespec)
ord=metaMDS(varespec,k=3,engine="monoMDS") #create ordination
km=kmeans(varespec,3) #kmeans clustering with 3 groups
fig=ordiplot(ord) 
ordiplot(fig,type="n") #plot ordination
text(fig,"sites",km$cluster,cex=0.8) #add cluster membership as text

That will give you something basic, like this:

Which is maybe not too pretty, but easily interpretable.