The heat map view

Image heatmap_output
Figure 33.63: The 2D heat map.

After the tool completes, a heat map like the one shown in (figure 33.63) 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 TMM normalized log CPM values, see RNA-Seq 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 33.63).

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 Features group has an option to "Optimize tree layout". This attempts to reorder the features, consistently with the tree, such that the most expressed features form a diagonal from the top-left to the bottom-right of the heat map.

The Samples group contains an "Order by:" dropdown that allows re-ordering of the columns of the heat map. Options within the dropdown include using the "Tree" to determine the sample ordering, showing the "Samples" in the order to which they were input to the tool, "Active Metadata layers" where the orders from selected Metadata layers are applied (see figure 33.64) or ordering the samples by associated metadata.

Image heat_map_metadata_ordered
Figure 33.64: A 2D heat map ordered by "Active metadata layers". Dataset analysed it from doi: 10.1534/g3.115.020982.

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

Image heatmap_rearrange_metadata
Figure 33.65: It is possible to re-order the values in a metadata layer by drag-and-drop.