{"output_id":"branch_trajectory","description":"Define a trajectory model given its branch network and the pseudotime of the cells on one of the branches","creates_trajectory":true,"required_args":["branch_network","branches","branch_progressions"],"optional_args":[]}
{"output_id":"cell_graph","description":"Constructs a trajectory using a graph between cells, by mapping cells onto a set of backbone cells.","creates_trajectory":true,"required_args":["cell_graph","to_keep"],"optional_args":["milestone_prefix"]}
{"output_id":"cluster_graph","description":"Constructs a trajectory using a cell grouping and a network between groups. Will use an existing grouping if it is present in the model.","creates_trajectory":true,"required_args":["milestone_network"],"optional_args":["grouping","explicit_splits"]}
{"output_id":"cyclic_trajectory","description":"Constructs a circular trajectory using the pseudotime values of each cell.","creates_trajectory":true,"required_args":["pseudotime"],"optional_args":["directed","do_scale_minmax"]}
{"output_id":"dimred","description":"Add or create a dimensionality reduction","creates_trajectory":false,"required_args":["dimred"],"optional_args":["dimred_milestones","dimred_trajectory_segments","expression_source"]}
{"output_id":"dimred_projection","description":"Constructs a trajectory by projecting cells within a dimensionality reduction onto a backbone formed by a milestone network. Optionally, a cell grouping can be given which will restrict the edges on which a cell can be projected.","creates_trajectory":true,"required_args":["milestone_network","dimred","dimred_milestones"],"optional_args":["milestone_ids","grouping","num_segments_per_edge"]}
{"output_id":"end_state_probabilities","description":"Multifurcating trajectory with end state probabilities","creates_trajectory":true,"required_args":["end_state_probabilities"],"optional_args":["pseudotime","do_scale_minmax"]}
{"output_id":"grouping","description":"Add a cell grouping to a data wrapper","creates_trajectory":false,"required_args":["grouping"],"optional_args":["group_ids"]}
{"output_id":"linear_trajectory","description":"Constructs a linear trajectory using the pseudotime values of each cell.","creates_trajectory":true,"required_args":["pseudotime"],"optional_args":["directed","do_scale_minmax"]}
{"output_id":"pseudotime","description":"Add or calculate pseudotime as distance from the root","creates_trajectory":false,"required_args":[],"optional_args":["pseudotime"]}
{"output_id":"root","description":"Root the trajectory","creates_trajectory":false,"required_args":[],"optional_args":["root_cell_id","root_milestone_id"]}
{"output_id":"timings","description":"Add count and normalised expression values to a model","creates_trajectory":false,"required_args":["timings"],"optional_args":[]}
{"output_id":"trajectory","description":"Define a trajectory model given its milestone network and milestone percentages or progressions","creates_trajectory":true,"required_args":["milestone_network","milestone_percentages","progressions"],"optional_args":["milestone_ids","divergence_regions"]}
{"output_id":"waypoints","description":"Add or create waypoints to a trajectory","creates_trajectory":false,"required_args":[],"optional_args":["n_waypoints","resolution"]}