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Creating a Two Way Matrix Tree Plot



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.



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

Selecting Items

Displaying a Gene Expression Value


Plot Functions

Profile Matching

Color by Gene Lists or Variables

Exporting an Image


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