CytoAnalyst Help

Pseudotime Trajectory Inference

What is Pseudotime Trajectory Inference?

Pseudotime trajectory inference is a method used to order cells based on their gene expression profiles. Cells are normally ordered along a trajectory that represents the progression of cells from one state to another.

To access the Pseudotime Trajectory Inference panel, click on the Time Trajectory tab on the Data and Analysis Panel.

Navigation to PseudoTime Trajectory Inference

Workflow

To perform pseudotime trajectory inference, you must have created embeddings. Visit the Embedding Analysis documentation to learn how to create embeddings.

Group by clusters

Group by metadata

Group by annotations

Enter name for pseudotime

Select method

Select embedding

Select how to group cells

Select clustering result

Select metadata field

Select annotations

Select start groups

Select end groups

Run pseudotime inference

System creates a job to infer pseudotime

Wait for job to complete

Visualize pseudotime trajectory

Create New Pseudotime Trajectory Inference

To create a new pseudotime trajectory inference, click on the New Time Trajectory button. A form will appear where you can enter the name for the pseudotime, select the method, embedding, and how to group cells.

New PseudoTime Trajectory Inference Form

The form contains the following fields:

  • Name: Enter a name for the pseudotime trajectory inference.

  • Method: Select the method you want to use for pseudotime trajectory inference. CytoAnalyst supports the following methods:

    • Slingshot: A method that uses principal curves to infer pseudotime.

  • Embedding: Select the embeddings on which you want to perform pseudotime trajectory inference. Visit the Embedding Analysis documentation to learn how to create embeddings.

  • Group Cells By: Select how you want to group cells for pseudotime trajectory inference. CytoAnalyst supports the following grouping options:

    • Clusters: Group cells by clusters.

    • Metadata: Group cells by metadata field.

    • Annotations: Group cells by annotations.

  • Cluster: Select the clustering result you want to use for grouping cells by clusters.

  • Metadata Field: Select the metadata field you want to use for grouping cells by metadata.

  • Annotations: Select the annotations you want to use for grouping cells by annotations.

  • Start Groups: Select the groups you want to use as the start of the pseudotime trajectory.

  • End Groups: Select the groups you want to use as the end of the pseudotime trajectory.

Existing Pseudotime Trajectory Inference

After running pseudotime trajectory inference, you can view the results in the Existing Time Trajectory table.

Existing PseudoTime Trajectory Inference

In this table, you can expand a pseudotime trajectory inference to:

  • Change the name of the pseudotime trajectory inference.

  • View the parameters used for the inference.

  • View the lineages of the pseudotime trajectory.

Visualization

Once you have created an existing pseudotime trajectory inference, the options for visualizing the pseudotime trajectory will be available on the Left Panel.

PseudoTime Trajectory Visualization

Pseudotime trajectory inferences results can be combined with other labels and data for visualization. To learn more about data visualization, see Data Visualization.

Last modified: 08 July 2025
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