įigure 1 SPADE trees with 100 clusters colored on the same parameter (TCR-beta) in five different software. If you’d like to read more on the theory and development of the SPADE algorithm, see the original literature. ![]() 1).Īs with a phylogenetic tree, similar clusters are grouped closer together, and dissimilar clusters are located more distally on the tree. ![]() The result is quite different from the two-dimensional plot of tSNE, and rather resembles a phylogenetic tree in its branching structure (Fig. Unlike tSNE, which is a dimensionality-reduction algorithm that presents a multidimensional dataset in 2 dimensions (tSNE-1 and tSNE-2), SPADE is a clustering and graph-layout algorithm. Like tSNE, SPADE extracts information across events in your data unsupervised and presents the result in a unique visual format. A favored algorithm in the flow cytometry community, SPADE is used when dealing with highly multidimensional or otherwise complex datasets. ![]() As a follow-up to our post on tSNE where we compared the speed of calculation in leading software packages, let’s consider the case of SPADE ( Spanning-tree Progression Analysis of Density-normalized Events).
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