And, there are number of genes that are low in cerebellum and high in other regions. There are a number of genes that are high in cerebellum for both species and pretty low in other regions. In the R lab you will have a look at the readily available color schemes and how to apply them. Here are heat maps using yellow and red for colors for the brain study. This looks much better and you can see patterns picked out by the clustering algorithm. (But for correlation distance, we should use z-scores.)Įuclidean distance: Color coding is by mean gene expressionĬorrelation distance: Color coding is by mean gene expression.Īnd here is the correlation distance heat map after converting to z-scores of the rows (genes).Ĭorrelation distance: Color coding after computing z-scores (row scaling) These are color-coded by expression values. The branches of the trees are rotated to create blocks in which the individual values are close in both directions. Finally, a color scheme is applied for the visualization and the expression matrix is displayed.

Then the branches of the dendrograms are rotated so that the blocks of 'high' and 'low' expression values are adjacent in the expression matrix. Usually correlation distance is used, but neither the clustering algorithm nor the distance need to be the same for rows and columns. First hierarchical clustering is done of both the rows and the columns of the expression matrix.

Heat maps are ways to simultaneously visualize clusters of samples and features, in our case genes.

Heatmap graphpad prism