For each pair of samples, the weighted Jaccard similarity between the two is computed. Let , denote the relative frequencies of the 'th clonotype in the first and second sample respectively. The weighted Jaccard similarity is defined as
The weighted Jaccard distance is defined as
The color gradient used by the heat map can be changed from the side panel. It is also possible to restrict the heat map to selected samples.
The heat map can be opened and saved as a stand-alone heat map by using the "Open as New Distance Heat Map" button. Various settings can be configured in the side panel of the stand-alone heat map, see http://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=_heat_map_view.html. Note that the "Open as New Distance Heat Map" button opens a heat map with "Columns" and "Rows" in the side panel, instead of the "Samples" and "Features" described in the linked manual.
The "Open as New Similarity Table" button opens a stand-alone table containing the Jaccard similarity between each pair of samples.