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20.7 Cluster
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[ Tree Select | Save and Print | Tree View ]

To perform clustering based on chemical similarity or any other data you must have an SDF file or table loaded into ICM.

OR

A data entry box as shown below will be displayed.

There are two clustering methods:

  1. A rigorous tree approach (advice to use this with 10000 compounds or less). This clustering algorithm consists of 2 steps: calculation of distance matrix (based on chemical fingerprints for chemical data) and the hieararchical clustering itself. Usually most time is being spent on first step.
  2. A less rigorous K-means approach. This option is quicker but the generated tree is not detalized down to the level of table rows. The elements within the table are colored and numbered according to their clustered group.

If your computer has enough memory we recomend you use the TREE method. It takes ~6 minutes to cluster 10000 compounds on a standard computer with 512Mb of memory.

NOTE If you wish to cluster a selection of a table; first select the compounds you wish to cluster (Ctrl A will select all or see the section of the manual entitled making table selections.

When using the TREE method select which linkage type you wish to use:

Check the option "Keep Distance Matrix" if you wish the Distance Matrix to be saved.

20.7.1 Tree Selection


A number of different selections can be made once the tree has been created.

Select Center Representatives From a Node.

To select the "center" representative compound or value from a cluster.

NOTE: Selections in the tree will be highlighted in blue in the tree and in the table.

Copy selection to new table.

All selections can be copied to a new table by:

20.7.2 Save and Print Tree


To save a tree

Option 1:

Option 2:

To save a tree as a picture

The image of the tree can also be saved to the clipboard.

To print the tree

20.7.3 Tree View


A number of changes to the tree view can be made by right clicking in the tree "free area" and selecting preferences as shown below.

A preferences window as shown below will be displayed.

Reverse Growth:

Distance Range:

Color Preferences:

Left: Fill Right: Color Lines

Left: Color lines to parent Right: Only labels

Increase or Decrease Line Spacing:

Increase or Decrease Line Width:

Change Font and Margins:

Change Label

To change the tree labeling (GLOBAL):

* Right click in the "free area" and select the Label/Sort option.

A window as shown below will be displayed:

To change the tree labeling (NODE):

Change Node Coloring

To change the color of a node:


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