# Representing and Inferring Single-Cell Trajectories

## Documentation for package ‘dynwrap’ version 1.3.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

.method_process_definition | Method process definition
add_attraction | Add attraction of cells using RNA velocity
add_branch_trajectory | Construct a trajectory given its branch network and the pseudotime of the cells on one of the branches.
add_cell_graph | Constructs a trajectory using a graph between cells, by mapping cells onto a set of backbone cells.
add_cell_waypoints | Add or select waypoint cells of a trajectory
add_cluster_graph | Constructs a trajectory using a cell grouping and a network between groups. Will use an existing grouping if it is present in the dataset.
add_cyclic_trajectory | Constructs a circular trajectory using the pseudotime values of each cell.
add_dimred | Add or create a dimensionality reduction
add_dimred_projection | Constructs a trajectory by projecting cells within a dimensionality reduction
add_end_state_probabilities | Constructs a multifurcating trajectory using end state probabilities
add_expression | Add count and normalised expression values to a dataset
add_feature_importance | Add a feature importance to a dataset
add_grouping | Add a cell grouping to a dataset
add_linear_trajectory | Constructs a linear trajectory using pseudotime values
add_prior_information | Add or compute prior information for a trajectory
add_pseudotime | Add or calculate pseudotime as distance from the root
add_regulatory_network | Add a GRN to a dynwrap object
add_root | Root the trajectory
add_root_using_expression | Root the trajectory
add_tde_overall | Add information on overall differentially expressed features
add_timings | Add timings to a trajectory
add_timing_checkpoint | Add timings to a trajectory
add_trajectory | Construct a trajectory given its milestone network and milestone percentages or progressions
add_waypoints | Add or create waypoints to a trajectory
allowed_inputs | All allowed inputs for a TI method
allowed_outputs | All allowed outputs for a TI method
calculate_attraction | Calculate the attraction of cells to other cells using velocity
calculate_average_by_group | Calculate average values of a matrix
calculate_geodesic_distances | Calculate geodesic distances between cells in a trajectory
calculate_pseudotime | Add or calculate pseudotime as distance from the root
calculate_trajectory_dimred | Layout the trajectory and its cells in 2 dimensions using a graph layout
classify_milestone_network | Classify a milestone network
compute_tented_geodesic_distances | Calculate geodesic distances between cells in a trajectory
convert_definition | Convert a definition loaded in from a yaml
convert_milestone_percentages_to_progressions | Conversion between milestone percentages and progressions
convert_progressions_to_milestone_percentages | Conversion between milestone percentages and progressions
create_ti_method_container | Create a TI method from a docker / singularity container
create_ti_method_definition | Create a TI method from a local method definition file
create_ti_method_r | Create a TI method from an R function wrapper
definition | Create a definition
def_author | Meta information on an author
def_container | Meta information on the container in which the wrapper resides
def_manuscript | Meta information on the manuscript
def_method | Define meta information on the TI method.
def_package | Meta information on the package in which the TI function resides
def_parameters | Meta information on the parameters of the TI method
def_wrapper | Meta information on the wrapper
determine_cell_trajectory_positions | Add or select waypoint cells of a trajectory
example_dataset | Example dataset
example_trajectory | Example trajectory
flip_edges | Flip a set of edges of the milestone network
gather_cells_at_milestones | Gather cells to their closest milestones
generate_parameter_documentation | Generate the parameter documentation of a method, use with @eval
generate_prior_information | Add or compute prior information for a trajectory
get_default_parameters | Get the default parameters of a method
get_dimred | Add or create a dimensionality reduction
get_expression | Add count and normalised expression values to a dataset
get_grouping | Add a cell grouping to a dataset
get_milestone_labelling | Label milestones either manually ('label_milestones') or using marker genes ('label_milestones_markers')
get_ti_methods | Return all TI that are installed in one or more packages
group_from_trajectory | Create a grouping from a trajectory
group_onto_nearest_milestones | Create a grouping from a trajectory
group_onto_trajectory_edges | Create a grouping from a trajectory
infer_trajectories | Infer one or more trajectories from a single-cell dataset
infer_trajectory | Infer one or more trajectories from a single-cell dataset
is_data_wrapper | A data wrapper for datasets and trajectories
is_rooted | Root the trajectory
is_ti_method | Create a definition
is_wrapper_with_dimred | Add or create a dimensionality reduction
is_wrapper_with_expression | Add count and normalised expression values to a dataset
is_wrapper_with_feature_importance | Add a feature importance to a dataset
is_wrapper_with_grouping | Add a cell grouping to a dataset
is_wrapper_with_milestone_labelling | Label milestones either manually ('label_milestones') or using marker genes ('label_milestones_markers')
is_wrapper_with_prior_information | Add or compute prior information for a trajectory
is_wrapper_with_timings | Add timings to a trajectory
is_wrapper_with_trajectory | Construct a trajectory given its milestone network and milestone percentages or progressions
is_wrapper_with_waypoints | Add or create waypoints to a trajectory
is_wrapper_with_waypoint_cells | Add or select waypoint cells of a trajectory
label_milestones | Label milestones either manually ('label_milestones') or using marker genes ('label_milestones_markers')
label_milestones_markers | Label milestones either manually ('label_milestones') or using marker genes ('label_milestones_markers')
priors | Metadata on priors
prior_usages | Metadata on prior usages
project_milestones | Project a trajectory onto a dimensionality reduction
project_trajectory | Project a trajectory onto a dimensionality reduction
project_waypoints | Project waypoints of a trajectory (e.g. milestones) into a space defined by cells (e.g. expression or a dimensionality reduction)
random_seed | Generate a random seed
remove_root | Root the trajectory
select_waypoints | Add or create waypoints to a trajectory
select_waypoint_cells | Add or select waypoint cells of a trajectory
simplify_igraph_network | Simplify an igraph network such that consecutive linear edges are removed
simplify_trajectory | Simplify a trajectory by removing transient milestones
trajectory_types | Metadata on the trajectory types
trajectory_type_dag | A DAG connecting different trajectory types
wrapper_types | Metadata on wrapper types
wrap_data | A data wrapper for datasets and trajectories
wrap_expression | Create a wrapper object with expression and counts