The Main Window 2D/3D Density Graphs


A 3D Density Graph

    2D and 3D Density Graphs constitute an extremely convenient way of assessing the respective positions of the clusters and the genes, in particular in combination with the transparent envelopes (hulls).
    The Density Graphs also yield a very powerful tool for estimating the desirable level of detail for the clustering, as they may suggest whether clusters should be split into parts (i.e., the level of detail / number of clusters should be increased), or whether clusters should be merged with the surrounding ones (i.e., the level of detail / number of clusters should be reduced).

    Density Graphs are displayed by selecting the Dn, Dl, or Dv mode of display of points representing the genes in the 2D button panel or 3D button panel, respectively. The three modes differ by the emphasis they put on high density areas in the image: the Dl (Density Light) and Dv (Density Very Light) modes reduce the influence of high-density areas, which is useful on large data sets where high-density areas are abundant.

    The position of the 3D Density Graph is adjusted as with other 3D graphs (see here).