Dendrogram is a tree-structure diagram visualizing affiliation between objects. It is used in many fields.
- In hierarchical clustering, it illustrates how cluster is constructed from a large set of data based on Hierarchical Clustering Analysis.
- In computational biology, it works together with heatmap to display how the objects (usually genes) are clustered.
- In phylogenetics, it is also called “phylogenetic tree”. It represents the relationship among various species during evolution.
Basic Dendrogram
To generate a dendrogram, you MUST index every node and arrange them in a hierarchical structure, like col(A) and col(B) in the below worksheet. We can read their affiliations as follow: node #1, #2, #3 and #4 are leaves, node #5 and #6 the upper level nodes, and #7 the root. All leaves are arranged evenly at the bottom axis and all nodes at the same level have the same distance from their parent node by default.
Optionally, you can further specify the distance between child and parent nodes, index for colormapping branches, and labels of nodes, like col(C), col(D) col(E).
Then you can use the following LabTalk script to generate a basic dendrogram
worksheet -p 108 tree
Tools that create Dendrograms in OriginPro
Hierarchical Cluster Analysis
The dendrogram is the result of built-in Hierarchical Cluster Analysis tool.
OriginPro 2020 now supports vertical, horizontal, and circular-orientation of dendrogram,
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- Select from menu Statistics: Multivariate Analysis: Hierarchical Cluster Analysis.
- In the Plot tab of the HCA dialog, choose to set Orientation radio button to “Vertical”, “Horizontal” or “Circular”.
The graph is embedded in the report sheet. For further customization, double click on the graph to open it in a separate graph window.
In the data highlighter mode, you can select a set of branches on the graph, the corresponding data in the worksheet will be highlighted.
Heatmap with Dendrogram App
Heat Map with Dendrogram App performs Hierarchical Cluster Analysis and plots dendrogram on the margins of heatmap.
Phylogenetics Tree App
If your data file is arranged in the construction of phylogenetic tree, Phylogenetic Tree App allows you to import it and plot it as rectangular phylogram.
Customize Dendrogram
Plot Details dialog
Like other graph types, almost all the customization controls can be found in the Plot Details dialog. Special for dendrogram, in the Label tab, you can
- Show Label for Leaves Only to hide parents’ labels
- Auto Hide Overlapped Label in case the nodes are clustered too densely.
Context menu
If you right-click on a node, a context menu list provides a quick access to some common operations for dendrogram. For example,
- Swap Subtrees. Available for all tools.
- Duplicate Branch to New Window will duplicate a branch from the selected node to a new window to read that part with more details. Available in built-in Hierarchical Cluster Analysis tool and Phylogenetics Tree App.
- Reroot a tree from the current node. Only support in Phylogenetics Tree App.
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