Heat Map

To access the Heat Map view, choose Graphs > Heat Map from the menu.

The Heat Map view is composed of several elements. The graphical display on the left is discussed in this topic. The toolbar tools above the graphical display and the Info Pane on the right are described in separate topics.

The Heat Map view uses color to display the signals (e.g., expression levels) of many genes across a number of experiments. The Heat Map display shows a grid of colored tiles. Each row in the grid corresponds to one gene, and each column represents a specific experiment.

The tree drawn to the left of the Heat Map display is called the Gene Tree and shows the clustering of genes as calculated by the selected clustering method.

By default, the experiments in your project are also clustered during Hierarchical Clustering. Experiment clusters can be viewed by clicking the Show Experiment Tree tool show_on_xaxis to display the Experiment Tree.

Note: You may choose to turn off the cluster experiments option through the Advanced Clustering dialog.

Gene names are displayed to the right of each corresponding row. If there is not enough space to display a complete list, a partial list is displayed, showing the genes closest to the position of your mouse. This abbreviated list updates as you move your mouse over the Heat Map, and the actual gene you are hovering over is underlined as shown below:

Use the vertical and horizontal scrollbars to the right and underneath the Heat Map display to scroll through the Heat Map.

At any time, you can un-select the current selection by doing one of the following:

• Select Edit > Clear Selection

• Click in any of the blank spaces outside of the Heat Map

• Right-click on the Heat Map and choose Clear Selection

Right-click on the Heat Map to access a variety of context menu commands:

When this many genes are selected	… these commands are available	Command description
≥ 0 genes	Edit Gene ‘x’ Notes	Equivalent to clicking on the “Notes (Edit)” link in the Details panel.
	Show Gene Table	Shortcut to Data > Show Gene Table.
	Remember Clustering Result	Shortcut to Clustering > Remember Clustering Result or to Remember Clustering Result tool ().
	Set [Experiment ‘x’] as Baseline Experiment	To set the experiment whose column you right-clicked on as the baseline to which other experiments will be compared.
	Select All	Shortcut to Edit > Select All.
	Copy Image	Shortcut to Edit > Copy Image of Graph or to the Copy Image tool ().
	Fit to View	Shortcut to the Fit to View tool ().
≥ 1 gene	Remember Gene Set	Shortcut to Data > Remember Selected [Genes, SNPs, Table Rows, etc.] and to the Remember Gene Set tool ().
	Clear Selection	Shortcut to Edit > Clear Selection.
	Export	Shortcut to File > Export Selected Genes.