Dendrograms are unique among the data objects of multiple variables graphs as they can only be created as part of the results from a hierarchical clustering analysis. Additionally, dendrograms can be presented as individual standalone graphs, or as objects added to a heat map (created by a hierarchical clustering analysis). The Dendrogram Options page of the format graph dialog allows you to add and customize these data objects on these graphs, and its content and layout will depend on whether the dendrogram is a standalone graph or as an addition to a heat map.

Required data structure

The only way to generate a dendrogram (either as a standalone graph or as a decoration on a heat map) is as part of the output from a hierarchical clustering analysis. There is no specific data structure required for your data as Prism will generate these graphs automatically when requested as part of the output of the hierarchical clustering analysis.

Format Options (Standalone dendrogram)

The checkbox at the top of the options page will allow you to toggle on or off the dendrogram on the graph. On macOS, this is a toggle as opposed to a checkbox.

Branches

This tab of the dendrogram options page allows you to customize the visual appearance of the branches (lines) of the dendrogram. If you performed the hierarchical clustering analysis without specifying a number of clusters (or cut height), then you will only be able to use the appearance option “Single Color”. However, if you chose to specify a number of clusters (or cut height) in the analysis parameters dialog, you may also choose the appearance option “Variable (by clusters)” which will allow you to assign different visual properties for each cluster in the generated dendrogram. These properties include:

•Color Scheme/Color - select a built-in color scheme to assign the color of the branches based on cluster, or choose a specific group and assign a custom color

•Transparency - set the transparency level of the branches of the dendrogram

•Thickness - define the line weight for the branches of the dendrogram

•Style - define the line pattern used for the branches of the dendrogram

•Orientation - Specify if the dendrogram should have a vertical distance axis and horizontal label axis (“Veritcal”) or a horizontal distance axis and a vertical label axis (“Horizontal”)

Labels

These options allow you to specify the appearance of the labels on the labels axis of the dendrogram. Labels type allows you to choose between variable values (default), letters (A, B, C…), or numbers (1, 2, 3…) for the labels. The starting at option indicates which label will be shown first (all labels before this one will be omitted from the graph), while the interval option indicates the frequency of labels to be displayed. For example, assume using numbers for labels. If the starting at option is set to 4, and the interval option is set to 3, then:

•Labels 1, 2, and 3 will not be shown

•Label 4 will be the first label shown

•Labels 5 and 6 will not be shown

•Label 7 will be shown, 8 and 9 will not be shown

•Label 10 will be shown, 11 and 12 will not be shown…

Also on this tab, you have the option to define the font as well as the rotation angle of the labels for the dendrogram.

Distance Axis

The distance axis is sometimes referred to as a “height” axis, and displays the distance between clusters as they’re formed during hierarchical clustering. These controls allow you to specify the visual properties of the distance axis, including:

•The color of the axis

•The transparency value of the axis

•The thickness of the axis

•The line style (pattern) of the axis

Note that currently there is no way to adjust the displayed range, ticks interval, or other properties of the distance axis.

Format Options (dendrograms as part of heat maps)

The checkbox at the top of the options page will allow you to toggle on or off the dendrogram on the graph. On macOS, this is a toggle as opposed to a checkbox. Note that toggling this option will either enable or disable all dendrograms on the graph. As part of the hierarchical clustering analysis, you may choose to perform clustering (and thus generate dendrograms) on rows, columns, or both. If for some reason you chose to perform clustering on both rows and columns, but wish to show only one or the other dendrogram on the associated heat map, do not use this primary toggle. Instead, set the corresponding dropdown menu (either Vertical axis or Horizontal axis) to “None” (more details below).

Each dendrogram added to a heat map is defined by the axis that it’s plotted on: either the “Vertical Axis” or the “Horizontal Axis”. This is because the heat map itself can map the rows of the data to either the horizontal axis or the vertical axis, and the same for the columns of the data. Thus, if the rows of the data are assigned to the horizontal axis of the heat map, then the dendrogram assigned to the horizontal axis will correspond to the clustering results performed on the rows of the data. If clustering was not performed on rows or columns in the hierarchical clustering analysis, then the corresponding dendrogram options will simply be disabled.

For each axis on which hierarchical clustering was performed, you have the option of specifying the general appearance of the dendrogram for that axis:

•None - disable (or hide) this dendrogram. Note that this is how you would disable only one dendrogram while leaving the other

•Single color - this will allow you to specify a single set of options (color, transparency, thickness, style) for all branches of the dendrogram

•Variable (by cluster) - this option allows you to specify options (color, transparency, thickness, style) individually for each cluster defined by the hierarchical clustering analysis for this dendrogram