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Creating a SOM Matrix Tree Plot



Tree plots are used to visualize clustering relationships. GeneLinkerô displays a tree plot in conjunction with a color matrix display of values, typically gene expression levels. A legend displays a color gradient and the scale from the minimum to maximum expression value range. The cluster tree appears to the right of the color array (when samples are clustered), or below the color matrix plot (when genes are clustered).



1. Click on a SOM experiment in the Experiments navigator. The item is highlighted.

2. Click the Matrix Tree Plot toolbar icon , or select Matrix Tree Plot from the Clustering menu, or right-click the item and select Matrix Tree Plot from the shortcut menu. A matrix tree plot of the SOM experiment is displayed.


Plot Indicators

As you move the mouse pointer over a gene or sample name, a gray bounding box is drawn around its column or row so you can easily see which tiles belong to it.

The names of one or more selected items (genes or samples) are highlighted in dark blue with white text. It is not possible to select genes and samples concurrently.

Hover the mouse pointer over a colored tile to see the gene name, sample name and value in a tooltip.


Interacting With the Plot

Selecting Items

Displaying a Gene Expression Value


Plot Functions

Profile Matching

Color by Gene Lists or Variables

Exporting a PNG Image


Customizing the Plot

Changing the Gradient Color and Scale

Resizing Cells in a Color Grid

Toggling the Color Grid On or Off


Related Topics:

Overview of Self-Organizing Maps (SOMs)

Tutorial 4: Self-Organizing Maps