# nat.nblast v1.6.5

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## NeuroAnatomy Toolbox ('nat') Extension for Assessing Neuron Similarity and Clustering

Extends package 'nat' (NeuroAnatomy Toolbox) by providing a collection of NBLAST-related functions for neuronal morphology comparison (Costa et al. (2016) <doi: 10.1016/j.neuron.2016.06.012>).

# nat.nblast

nat.nblast is part of the NeuroAnatomy Toolbox suite of R packages.

## Quick Start

For the impatient ...

# install
if (!require("devtools")) install.packages("devtools")
devtools::install_github(c("natverse/nat", "natverse/nat.nblast"))

# use
library(nat.nblast)

# run examples for search
example("nblast")

# run examples for clustering
example("nhclust")

# get overview help for package
?nat.nblast
# help for functions
?nblast
?nhclust

# run tests
library(testthat)
test_package("nat.nblast")


## Introduction

This R package implements the NBLAST neuron similarity algorithm described in

Costa M, Manton JD, Ostrovsky AD, Prohaska S, Jefferis GS. NBLAST: Rapid, Sensitive Comparison of Neuronal Structure and Construction of Neuron Family Databases.Neuron. 2016 Jul 20;91(2):293-311. doi: 10.1016/j.neuron.2016.06.012.

In addition to basic pairwise comparison, the package implements search of databases of neurons. There is also support for all x all comparison for a group of neurons. This can produce a distance matrix suitable for hierarchical clustering, which is also implemented in the package.

These tools are designed as an addon for the NeuroAnatomy Toolbox (nat) R package, which will be installed as dependency.

You will probably find the following online documentation helpful:

## Installation

This package has been released to CRAN (since v1.5), but we generally recommend installing the development version from GitHub, especially if you notice a bug.

### CRAN release

install.packages("nat.nblast")


### Development version

Use devtools to install the development version:

# install devtools if required
if (!require("devtools")) install.packages("devtools")
# then nat.nblast
devtools::install_github("natverse/nat.nblast")


Note that this will also update the nat package to the latest development version from github. Windows users need Rtools to install this way.

## Functions in nat.nblast

 Name Description smat.fcwb Scoring matrices for neuron similarities in FCWB template brain fill_pairs_sparse_score_mat Add forwards, reverse and self scores for a pair of neurons to a sparse score matrix subset.hclust Return the labels of items in 1 or more groups cut from hclust object [ Extract parts of a sparse spam matrix nat.nblast-package Neuron similarity, search and clustering tools show_similarity Display two neurons with segments in the query coloured by similarity sub_dist_mat Convert (a subset of) a raw score matrix to a distance matrix sub_score_mat Return scores (or distances) for given query and target neurons plot3d.hclust Methods to identify and plot groups of neurons cut from an hclust object neuron_pairs Utility function to generate all or random pairs of neurons sparse_score_mat Convert a subset of a square score matrix to a sparse representation nhclust Cluster a set of neurons nblast Calculate similarity score for neuron morphologies nblast_allbyall Wrapper function to compute all by all NBLAST scores for a set of neurons NeuriteBlast Produce similarity score for neuron morphologies calc_score_matrix Calculate scoring matrix from probability matrices for matching and non-matching sets of neurons diagonal Extract diagonal terms from a variety of matrix types calc_dists_dotprods Calculate distances and dot products between two sets of neurons create_scoringmatrix Create a scoring matrix given matching and non-matching sets of neurons WeightedNNBasedLinesetMatching Compute point & tangent vector similarity score between two linesets fctraces20 20 traced Drosophila neurons from Chiang et al 2011 calc_prob_mat Calculate probability matrix from distances and dot products between neuron segments fill_in_sparse_score_mat Add one or more submatrices to a sparse score matrix No Results!