Tutorials¶

Run ONTraC¶

See the command line tutorial for details if you want to use ONTraC in command-line mode.
See the interactive tutorial for details if you want to use ONTraC in a Jupyter notebook.
See the interoperate with Giotto tutorial for details if you want to use ONTraC within the Giotto ecosystem.
See the IO files tutorial for details about input and output files.

Downstream Analysis¶

Visualization¶

See the visualization tutorial for details about how to visualize ONTraC results.

Spatial Trajectory-based Analysis¶

See spatial trajectory-based analysis tutorial for various features changes along spatial trajectory (cell-level NT scores):

Cell type composition
Gene expression
Regulon activity
Other features

Niche Clusters¶

Niche clusters are one of the intermediate results of ONTraC. If you want to treat them as a spatial clustering result, please follow the niche cluster tutorial.

Multiple Samples¶

ONTraC can generate consistent spatial trajectories (NT score) across multiple slices/samples.

Here is a demonstration example using the MERFISH mouse primary motor cortex dataset.

Others¶

Parameters¶

Please refer to Parameters Explanation for detailed information about each parameter.