## Package Overview

Provides an overview of key functions and classes

nat.nblast-package

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

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