Re-root BANC neuron skeleton at soma — banc

This function re-roots a neuron skeleton represented as a neuron object at the location of the corresponding soma in the roots data frame. It uses the root_id in the skeleton object to identify the soma location.

Usage

banc_reroot(x, id = NULL, roots = NULL, estimate = TRUE, ...)

# S3 method for class 'neuron'
banc_reroot(x, id = NULL, roots = NULL, estimate = TRUE, ...)

# S3 method for class 'neuronlist'
banc_reroot(x, id = NULL, roots = NULL, estimate = TRUE, ...)

Arguments

x: A banc.neurite object representing the neuron skeleton.
id: (Optional) The root_id of the neuron in the roots data frame. If NULL, it will be taken from the x$root_id slot.
roots: A data frame containing information about root points, i.e. nuclei obtained using bancr:::banc_roots(). This data frame is assumed to have columns named root_id and root_position_nm, where root_position_nm specifies the 3D coordinates of the soma for each root_id.
estimate: if TRUE and nucleus position is not in roots, then root is estimated as a leaf node furthest outside of the brain neuropil.
...: Methods passed to nat::nlapply.

Value

The function returns the re-rooted neuron object.

Examples

if (FALSE) { # \dontrun{
x <- banc_read_l2skel(..., simplify = FALSE)
roots <- bancr:::banc_roots()
re-rooted_neuron <- banc_reroot(x, roots = roots)
} # }