The heat map view

Image heatmap_output
Figure 28.35: The 2D heat map.

After the tool completes, a heat map like the one shown in (figure 28.35) is produced. In the heat map each row corresponds to a feature and each column to a sample. The color in the $ i$'th row and $ j$'th column reflects the expression level of feature $ i$ in sample $ j$ (the color scale can be set in the side panel). The expression values used are normalized log CPM values, see TMM Normalization.

There are a number of options to change the appearance of the heat map. At the top of the Side Panel, you find the Heat map group (see figure 28.35).

Below you find the Samples and Features groups. They contain options to show names, color legends, and trees above or below the heat map. The tree options also control the Tree size, including the option of showing the full tree, no matter how much space it will use.

The Metadata group makes it possible to visualize metadata associated with the Expression tracks: