sub_dist_mat: Convert (a subset of) a raw score matrix to a distance matrix

In nat.nblast: NeuroAnatomy Toolbox ('nat') Extension for Assessing Neuron Similarity and Clustering

Convert (a subset of) a raw score matrix to a distance matrix

Description

This function can convert a raw score matrix returned by nblast into a square distance matrix or dist object. It can be used with file-backed matrices as well as regular R matrices resident in memory.

Usage

sub_dist_mat(
  neuron_names,
  scoremat = NULL,
  form = c("matrix", "dist"),
  maxneurons = NA
)

Arguments

neuron_names	character vector of neuron identifiers.
scoremat	score matrix to use (see sub_score_mat for details of default).
form	the type of object to return.
maxneurons	set this to a sensible value to avoid loading huge (order N^2) distances directly into memory.

Details

Note that if neuron_names is missing then the rownames of scoremat will be used i.e. every neuron in scoremat will be used.

Value

return An object of class matrix or dist (as determined by the form argument), corresponding to a subset of the distance matrix

See Also

Other scoremats: nhclust()

nat.nblast documentation built on Aug. 18, 2025, 5:25 p.m.