The Create Heat Map tool simultaneously clusters samples and features, showing a two dimensional heat map of expression values. Each column corresponds to one sample, and each row corresponds to a feature (a gene or a transcript). The samples and features are both hierarchically clustered. Known metadata about each sample is added as an overlay.
The Create Heat Map for RNA-Seq tool uses the TMM normalization (described in TMM Normalization) to make samples comparable, then does a z-score normalization to make features comparable.