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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.

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Version

Install

install.packages('nat.nblast')

Monthly Downloads

162

Version

1.6.5

License

GPL-3

Issues

Pull Requests

Stars

Forks

Maintainer

James Manton

Last Published

January 23rd, 2020

Functions in nat.nblast (1.6.5)

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