TIP: Dendrogram is a tree diagram used to illustrate the arrangement of the clusters produced by hierarchical clustering.
The dendrogram is a visual representation of the spot correlation data. The individual spots are arranged along the bottom of the dendrogram and referred to as leaf nodes. Spot clusters are formed by joining individual spots or existing spot clusters with the join point referred to as a node. At each stage distances between clusters are recomputed by the Lance Williams dissimilarity update formula according to the particular clustering method being used.
In addition, the vertical axis is labelled distance and refers to a distance measure between spots or spot clusters.We also provided other option to calculate distance, such as Euclidean, Maximum, Manhattan, Canberra and so forth and some other methods to conduct hierarchical cluster. However the closer two points are, the more they will be assigned to same group. In each step the most correlated point will be in the same group until every point are in one big group.
Here is the option I use to plot the picture above, here we use dendrogram.txt as data file.