Package index • nat.nblast

Package Overview

Provides an overview of key functions and classes

nat.nblast-package nat.nblast: Neuron similarity, search and clustering tools

Key functions

The main entry points to neuron search and clustering

nblast(): Calculate similarity score for neuron morphologies

nblast_allbyall(): Wrapper function to compute all by all NBLAST scores for a set of neurons

nhclust(): Cluster a set of neurons

Plotting results

Visualise pairwise neuron search or clustering results

plot3d(<hclust>): Methods to identify and plot groups of neurons cut from an hclust object

show_similarity(): Display two neurons with segments in the query coloured by similarity

subset(<hclust>): Return the labels of items in 1 or more groups cut from hclust object

Scoring Matrices

Calculate the scoring matrices that define NBLAST similarity

create_scoringmatrix(): Create a scoring matrix given matching and non-matching sets of neurons

calc_score_matrix(): Calculate scoring matrix from probability matrices for matching and non-matching sets of neurons

calc_prob_mat(): Calculate probability matrix from distances and dot products between neuron segments

calc_dists_dotprods(): Calculate distances and dot products between two sets of neurons

smat.fcwb smat_alpha.fcwb: Scoring matrices for neuron similarities in FCWB template brain

Mid level functions for result matrices

Functions that you might use to manipulate matrices containing all by all NBLAST results for use with other clustering strategies (besides nhclust)

sub_score_mat(): Return scores (or distances) for given query and target neurons

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

sparse_score_mat(): Convert a subset of a square score matrix to a sparse representation

Low level search functions

Intended for developer use

NeuriteBlast(): Produce similarity score for neuron morphologies

neuron_pairs(): Utility function to generate all or random pairs of neurons

WeightedNNBasedLinesetMatching(): Compute point & tangent vector similarity score between two linesets

fctraces20: 20 traced Drosophila neurons from Chiang et al 2011

Matrix utility functions

Intended for developer use

diagonal(): Extract diagonal terms from a variety of matrix types

`[`(<spam>,<character>,<character>,<logical>) `[`(<spam>,<character>,<character>,<missing>) `[`(<spam>,<character>,<missing>,<logical>) `[`(<spam>,<character>,<missing>,<missing>) `[`(<spam>,<missing>,<character>,<logical>) `[`(<spam>,<missing>,<character>,<missing>): Extract parts of a sparse spam matrix

fill_in_sparse_score_mat(): Add one or more submatrices to a sparse score matrix

fill_pairs_sparse_score_mat(): Add forwards, reverse and self scores for a pair of neurons to a sparse score matrix