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Creating a Two Way Matrix Tree Plot
Overview
A two way matrix tree plot is useful for visualizing the results of two clustering experiments simultaneously. One must be based on genes, and the other on samples and both must be derived from the same original dataset.
Actions
1. Press and hold the <Ctrl> key, and then click on two clustering experiments under the same original dataset in the Experiments navigator. One must be sample-based; the other gene-based. Both items are highlighted.
2. Click the Two
Way Matrix Tree Plot toolbar icon 
, or select Two Way Matrix Tree Plot from the Clustering menu, or right-click on of
the highlighted items and select Two
Way Matrix Tree Plot from the shortcut menu. The
plot is displayed with the sample clusters on the right side and the gene
clusters on the bottom, relative to the color matrix portion of the plot.
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 which gene or column.
As you move the mouse pointer over the dendrogram portion of the plot, the gray bounding box surrounds the genes that are in that node cluster and a tooltip is displayed listing the number of members and a cluster merge distance reference value.
The name of a selected item (genes or samples) is highlighted in dark blue with white text. One or more items can be selected, however, it is not possible to select genes and samples concurrently.
Interacting With the Plot
Displaying a Gene Expression Value
Plot Functions
Color by Gene Lists or Variables
Customizing the Plot
Changing the Gradient Color and Scale
Resizing Cells in a Color Grid
Toggling the Color Grid On or Off
Related Topic:
Creating a Summary Statistics Chart