Clonotype tracking heatmap details

[LJhows]

No information is provided on the VDJ tools documentation regarding the details of the analysis output for the clonotype tracking heatmap function. The output graph key simply says "value" not specific like the "column z-score" for the segment usage heat map. also details missing that are included for the segment usage heat map, e.g. "weighted Variable usage profiles are used, hierarchical clustering is performed using euclidean distance."

If you could add this extra detail that would be greatly appreciated!

[mikessh]

The Z scores are computed by the heatmap.2 function that makes the plot (see e.g. https://www.rdocumentation.org/packages/gplots/versions/3.0.1/topics/heatmap.2). Typically for a vector X one can obtain Z scores by normalizing them to 0 mean and 1 standard deviation:

Z = (X - mean(X)) / sd(X)