How do I color a dendrogram in R?

Table of Contents

Step 1: Install Packages.
Step 2: Load Data.
Step 3: Normalize Data and Create Dendrogram.
Step 4: Extract Dendrogram Segment Data Using ggdendro.
Step 5: Generate a Custom Color Palette for Dendrogram Ends Based on Metadata Variables using RColorBrewer (Optional)
Step 6: Plot your Custom-Colored Dendrogram!

How do I plot a dendrogram in R?

As you already know, the standard R function plot. hclust() can be used to draw a dendrogram from the results of hierarchical clustering analyses (computed using hclust() function). A simplified format is: plot(x, labels = NULL, hang = 0.1, main = “Cluster dendrogram”, sub = NULL, xlab = NULL, ylab = “Height”.)

What do colors in dendrogram mean?

Colors all the descendent links below a cluster node k the same color if k is the first node below the cut threshold t. All links connecting nodes with distances greater than or equal to the threshold are colored blue. If t is less than or equal to zero, all nodes are colored blue.

What is Cutree function in R?

Remember from the video that cutree() is the R function that cuts a hierarchical model. The h and k arguments to cutree() allow you to cut the tree based on a certain height h or a certain number of clusters k.

How do you plot hierarchical clustering in R?

The algorithm is as follows:

Make each data point in a single point cluster that forms N clusters.
Take the two closest data points and make them one cluster that forms N-1 clusters.
Take the two closest clusters and make them one cluster that forms N-2 clusters.
Repeat steps 3 until there is only one cluster.

How do you read a hierarchical cluster?

The key to interpreting a hierarchical cluster analysis is to look at the point at which any given pair of cards “join together” in the tree diagram. Cards that join together sooner are more similar to each other than those that join together later.

What is the difference between Cladogram and dendrogram?

Dendrogram is a broad term used to represent a phylogenetic tree. More precisely, “dendrogram” is a generic term applied to any type of phylogenetic tree (scaled or unscaled). Cladogram is a representation of the ancestor‐to‐descendant relationship through a branching tree.

How do you interpret hierarchical cluster analysis results?

How do you read cluster analysis?

The higher the similarity level, the more similar the observations are in each cluster. The lower the distance level, the closer the observations are in each cluster. Ideally, the clusters should have a relatively high similarity level and a relatively low distance level.

How do you determine the number of clusters in a dendrogram?

In the dendrogram locate the largest vertical difference between nodes, and in the middle pass an horizontal line. The number of vertical lines intersecting it is the optimal number of clusters (when affinity is calculated using the method set in linkage).