Representing and Inferring Single-Cell Trajectories

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Documentation for package ‘dynwrap’ version 1.2.4

• DESCRIPTION file.
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.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
dynwrap	Inferring and adapting single-cell trajectories
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