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There configuration dialog presents two options.

1. Dimensionality of reduced space. This option specifies the number of UMAP dimensions that the original data are reduced to, in order to learn the trajectory tree (dimensionality of original data equals the number of genes). Default is two, meaning that the trajectory plot will be draw in two dimensions. To get a 3D trajectory plot, increase this option to 3.
2. Scaling. Normalized expression values can be further transformed by scaling to unit variance and zero mean (i.e. converting to Z score). The use of this option is recommended. 

Trajectory Result

Result of running Trajectory analysis in Partek Flow is the Trajectory result data node. Double clicking on the node opens a Data Viewer window with the trajectory plot (Figure xxx). Cell trajectory graph. Blue dots are individual cells (total count is displayed in the upper right). Black line represents the structure of the trajectory graph. Gray circles are nodes or leaves. The axes represent UMAP coordinates.

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