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>).
Readme
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:
- https://natverse.github.io/nat.nblast - Online documentation for this R package
- http://jefferislab.org/si/nblast - Overview of NBLAST algorithm and online tools
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 | |
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Vignettes of nat.nblast
Name | ||
NBLAST-Clustering.Rmd | ||
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Details
Type | Package |
URL | https://github.com/natverse/nat.nblast, https://natverse.github.io |
BugReports | https://github.com/natverse/nat.nblast/issues |
License | GPL-3 |
LazyData | yes |
VignetteBuilder | knitr |
RoxygenNote | 7.0.2 |
Language | en-GB |
Encoding | UTF-8 |
NeedsCompilation | no |
Packaged | 2020-01-23 13:47:22 UTC; James Manton |
Repository | CRAN |
Date/Publication | 2020-01-23 14:10:05 UTC |
suggests | bigmemory , ff , knitr , rmarkdown , spelling , testthat |
imports | dendroextras , nabor , plyr , spam |
depends | methods , nat (>= 1.5.12) , R (>= 2.15.1) , rgl |
Contributors | Gregory Jefferis |
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