# calculate_geodesic_distances: Calculate geodesic distances between cells in a trajectory In dynwrap: Representing and Inferring Single-Cell Trajectories

 calculate_geodesic_distances R Documentation

## Calculate geodesic distances between cells in a trajectory

### Description

Will calculate geodesic distances between cells within a trajectory. To speed things up, only the distances with a set of waypoint cells are calculated.

### Usage

``````calculate_geodesic_distances(
trajectory,
waypoint_cells = NULL,
waypoint_milestone_percentages = NULL,
directed = FALSE
)

compute_tented_geodesic_distances(
trajectory,
waypoint_cells = NULL,
waypoint_milestone_percentages = NULL
)
``````

### Arguments

 `trajectory` The trajectory as created by `infer_trajectory()` or `add_trajectory()` `waypoint_cells` A vector of waypoint cells. Only the geodesic distances between waypoint cells and all other cells will be calculated. `waypoint_milestone_percentages` The milestone percentages of non-cell waypoints, containing waypoint_id, milestone_id and percentage columns `directed` Take into account the directions of the milestone edges. The cells that cannot be reached from a particular waypoint will have distance infinity. You can also give a character, if it is "forward" it will look forward, if it is "reverse" it will look in the reversed direction

### Details

The geodesic distance takes into account the length of an edge regions of delayed commitment.

### Value

A matrix containing geodesic distances between each waypoint cell (rows) and cell (columns)

### Examples

``````geodesic_distances <- calculate_geodesic_distances(example_trajectory)
geodesic_distances[1:10, 1:10]

``````

dynwrap documentation built on July 26, 2023, 5:15 p.m.