Project a trajectory onto a dimensionality reduction
project_trajectory(
trajectory,
dimred,
waypoints = select_waypoints(trajectory),
trajectory_projection_sd = sum(trajectory$milestone_network$length) * 0.05
)project_milestones(
trajectory,
dimred,
trajectory_projection_sd = sum(trajectory$milestone_network$length) * 0.05
)
A list containing
dimred_segment_points: The dimensionality reduction of a set of points along the trajectory. A matrix with the position of points (rows) in the dimensions (columns)
dimred_segment_progressions The progressions of the points. A dataframe containing the from and to milestones, and their progression. Has the same number of rows as dimred_segment_points
dimred_milestones: The dimensionality reduction of the milestones. A matrix with the position of milestones (rows) in the dimensions (columns)
These objects can be given to add_dimred()
The trajectory as created by infer_trajectory() or add_trajectory()
The dimensionality reduction of the cells. A matrix with the positions of cells (rows) in the dimensions (columns)
A set of waypoints, which can be created by select_waypoints(). It is a list containing:
waypoints: a dataframe containing in the very least the waypoint_id
milestone_percentages: the positions of waypoints withing the trajectory
geodesic_distances: matrix with precalculated geodesic distances between waypoints (rows) and cells (columns), optional
The standard deviation of the gaussian kernel
add_dimred()