# This Package Discovers Directionality in Time and Pseudo-times Series of Gene Expression Patterns

## Documentation for package ‘TrajectoryGeometry’ version 1.6.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

analyseBranchPoint | Analyse branch point.
analyseSingleCellTrajectory | Analyse a single cell trajectory.
chol_answers | chol_answers
chol_attributes | chol_attributes
chol_branch_point_results | chol_branch_point_results
chol_pseudo_time | chol_pseudo_time
chol_pseudo_time_normalised | chol_pseudo_time_normalised
circleOnTheUnitSphere | Circle on the unit sphere
crooked_path | Crooked path
crooked_path_center | Crooked path center
crooked_path_projection | Crooked path projection
crooked_path_radius | Crooked path radius
distanceBetweenTrajectories | Get distances between trajectories.
findSphereClusterCenter | Find a center for points on the unit sphere
findSphericalDistance | Find the spherical distance from a given point to a set of points.
generateRandomPaths | Produce random paths modeled on a given path
generateRandomUnitVector | Generate random unit vector.
getDistanceDataForPaths | Produce distance statistics for random paths
getSphericalData | This is a simplified wrapper for pathToSphericalData
getStepLengths | Find the step lengths:
hep_answers | hep_answers
hep_attributes | hep_attributes
hep_pseudo_time | hep_pseudo_time
hep_pseudo_time_normalised | hep_pseudo_time_normalised
orthonormalBasis | Find an orthonormal basis in dimension 3
oscillation | Oscillation
pathProgression | Measure a path's progression
pathToSphericalData | Find the spherical data for a given path
plotPathProjectionCenterAndCircle | Plot a path, its projection, its center and its circle
projectPathToSphere | Project a path onto the unit sphere
samplePath | Sample a path from single cell data
single_cell_matrix | single_cell_matrix
straight_path | Straight path
straight_path_center | Straight path center
straight_path_projection | Straight path projection
straight_path_radius | Straight path radius
testPathForDirectionality | Test a path for directionality
visualiseBranchPointStats | Visualise Branch Point Stats
visualiseTrajectoryStats | Visualise Trajectory Stats