Examples

This section contains various short examples showcasing core moscot functionality.

Problems

This section contains various examples how to handle moscot.problems.

• Tagged arrays
  • Imports and data loading
  • Prepare the problem
  • Attributes
  • Modifying the tags
• Passing callbacks in prepare()
  • Imports and data loading
  • Spatial normalization
  • Passing callbacks
• Custom cost matrices
  • Imports and data loading
  • Prepare the problem
  • Setting cost functions individually for each term
  • Passing cost matrices manually
  • Cost matrices in the obsp layer
• Adding and removing problems
  • Imports and data loading
  • Prepare and solve the problem
  • Re-solving a subproblem
• Subset policy
  • Imports and data loading
  • TemporalProblem policies
• Handling marginals
  • Imports and data loading
  • Uniform marginals
  • User-defined marginals
• Annotation mapping
  • Imports and data loading
  • Cluster the data
  • Prepare and solve the problem
  • Create the annotation mapping of leiden clusters
• Problems
  • Alignment Problem
  • Lineage Problem
  • Spatio Temporal Problem
  • Temporal Problem

Solvers

This section contains various examples on how to handle moscot.solvers.

• Linear problems
• Linear problems (advanced)
• Quadratic problems
• Quadratic problems (advanced)

Plotting

This section contains various examples from the moscot.plotting module.

• Pull/push distributions
• Cell transitions
• Sankey diagram