R Graphical Manual

Last data update: 2014.03.03

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R Release (3.2.3)
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Results 1 - 10 of 23 found.
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sparse_score_mat (Package: nat.nblast) : Convert a subset of a square score matrix to a sparse representation

This can be useful for storing raw forwards and reverse NBLAST scores for a set of neurons without having to store all the uncomputed elements in the full score matrix.

● Data Source: CranContrib
● Keywords:
● Alias: sparse_score_mat
● 0 images

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

Calls nblast to compute the actual scores. Can accept either a neuronlist or neuron names as a character vector. This is a thin wrapper around nblast and its main advantage is the option of "mean" normalisation for forward and reverse scores, which is the most sensible input to give to a clustering algorithm as well as the choice of returning a distance matrix.

● Data Source: CranContrib
● Keywords:
● Alias: nblast_allbyall, nblast_allbyall.character, nblast_allbyall.neuronlist
● 0 images

subset.hclust (Package: nat.nblast) : Return the labels of items in 1 or more groups cut from hclust object

Return the labels of items in 1 or more groups cut from hclust object

● Data Source: CranContrib
● Keywords:
● Alias: subset.hclust
● 0 images

fctraces20 (Package: nat.nblast) : 20 traced Drosophila neurons from Chiang et al 2011

This R list (which has additional class neuronlist) contains 15 skeletonized Drosophila neurons as dotprops objects. Original data is due to Chiang et al. [1], who have generously shared their raw data at http://flycircuit.tw. Automated tracing of neuron skeletons was carried out by Lee et al [2]. Image registration and further processing was carried out by Greg Jefferis, Marta Costa and James Manton[3].

● Data Source: CranContrib
● Keywords:
● Alias: fctraces20
● 0 images

WeightedNNBasedLinesetMatching (Package: nat.nblast) : Compute point & tangent vector similarity score between two linesets

WeightedNNBasedLinesetMatching will work with 2 objects of class dotprops or neuron. The code to calculate scores directly for neuron objects gives broadly comparable scores to that for dotprops objects, but has been lightly tested. Furthermore only objects in dotprops form were used in the constriction of the scoring matrices distributed in this package. It is therefore recommended to convert neuron objects to dotprops objects using the dotprops function.

● Data Source: CranContrib
● Keywords:
● Alias: WeightedNNBasedLinesetMatching, WeightedNNBasedLinesetMatching.dotprops, WeightedNNBasedLinesetMatching.neuron
● 0 images

nblast (Package: nat.nblast) : Calculate similarity score for neuron morphologies

Uses the NBLAST algorithm that compares the morphology of two neurons. For more control over the parameters of the algorithm, see the arguments of NeuriteBlast.

● Data Source: CranContrib
● Keywords:
● Alias: nblast
● 0 images

sub_dist_mat (Package: nat.nblast) : Convert (a subset of) a raw score matrix to a distance matrix

This function can convert a raw score matrix returned by nblast into a square distance matrix or dist object. It can be used with file-backed matrices as well as regular R matrices resident in memory.

● Data Source: CranContrib
● Keywords:
● Alias: sub_dist_mat
● 0 images

plot3d.hclust (Package: nat.nblast) : Methods to identify and plot groups of neurons cut from an hclust object

plot3d.hclust uses plot3d to plot neurons from each group, cut from the hclust object, by colour.

● Data Source: CranContrib
● Keywords:
● Alias: plot3d.hclust
● 0 images

[ (Package: nat.nblast) : Extract parts of a sparse code{spam

Extract parts of a sparse spam matrix

● Data Source: CranContrib
● Keywords:
● Alias: [, [,spam,character,character,logical-method, [,spam,character,character,missing-method, [,spam,character,missing,logical-method, [,spam,character,missing,missing-method, [,spam,missing,character,logical-method, [,spam,missing,character,missing-method
● 0 images

show_similarity (Package: nat.nblast) : Display two neurons with segments coloured by similarity

Display two neurons with segments coloured by similarity

● Data Source: CranContrib
● Keywords:
● Alias: show_similarity
● 0 images