Running Trajectory Analysis
To run Trajectory analysis tool, select the Normalized counts data node (or equivalent) and go to the toolbox: Exploratory analysis > Trajectory analysis
There configuration dialog presents two options.
- 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.
- 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 shows position of each cell (blue dot) with respect to the UMAP coordinates (axes). Cell trajectories (one or more, depending on the data set) are depicted as black lines. Gray circles are trajectory nodes (i.e. cell communities).
Figure 1. 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.
To show / hide cell trajectory tree and trajectory nodes, use the Extra data option on the Content card (Figure xxx).
Figure 2. Extra data card enables the user to turn the trajectory tree and the trajectory nodes on or off
Additional Assistance
If you need additional assistance, please visit our support page to submit a help ticket or find phone numbers for regional support.
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Overview
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