R: AFM image networks analysis class

AFMImageNetworksAnalysis-class {AFM}

R Documentation

AFM image networks analysis class

Description

A S4 class to handle the networks calculation

Usage

AFMImageNetworksAnalysis()

## S4 method for signature 'AFMImageNetworksAnalysis'
initialize(
  .Object,
  vertexHashsize,
  binaryAFMImage,
  binaryAFMImageWithCircles,
  circlesTable,
  edgesTable,
  fusionedNodesCorrespondance,
  fusionedNodesEdgesTable,
  isolatedNodesList,
  heightNetworksslider,
  filterNetworkssliderMin,
  filterNetworkssliderMax,
  smallBranchesTreatment,
  originalGraph,
  skeletonGraph,
  shortestPaths,
  networksCharacteristics,
  holes,
  holesCharacteristics,
  graphEvcent,
  graphBetweenness,
  libVersion
)

AFMImageNetworksAnalysis()

Arguments

`.Object`	an AFMImageNetworksAnalysis Class
`vertexHashsize`	hash to transform coordinates to vertexId
`binaryAFMImage`	the AFMImage after transformation before analysis
`binaryAFMImageWithCircles`	the AFMImage after transformation with the spotted circles
`circlesTable`	a data.table of identified circles
`edgesTable`	a data.table of edges
`fusionedNodesCorrespondance`	a data.table of correspon
`fusionedNodesEdgesTable`	a data.table of corresponsdance between intial node and fusioned node
`isolatedNodesList`	a data.table of isolated nodes
`heightNetworksslider`	used multiplier of heights to facilitate analysis
`filterNetworkssliderMin`	used filter minimum value to facilitate analysis
`filterNetworkssliderMax`	used filter maximum value to facilitate analysis
`smallBranchesTreatment`	boolean - smallest circle used or not
`originalGraph`	a list of `igraph`
`skeletonGraph`	a list of `igraph`
`shortestPaths`	a data.table of shortest path
`networksCharacteristics`	a data.table to store the skeleton graph characteristics
`holes`	a data.table to store the cluster number of each point
`holesCharacteristics`	a data.table to summarize the data about holes
`graphEvcent`	an array to store Evcent
`graphBetweenness`	an array to store the graph betweenness
`libVersion`	version of the AFM library used to perform the analysis

Slots

vertexHashsize: hash to transform coordinates to vertexId
binaryAFMImage: the AFMImage after transformation before analysis
binaryAFMImageWithCircles: the AFMImage after transformation with the spotted circles
circlesTable: a data.table of identified circles
edgesTable: a data.table of edges
fusionedNodesCorrespondance: a data.table of corresponsdance between intial node and fusioned node
fusionedNodesEdgesTable: a data.table of nodes fusioned because of intersecting
isolatedNodesTable: a data.table of isolated nodes
heightNetworksslider: used multiplier of heights to facilitate analysis
filterNetworkssliderMin: used filter minimum value to facilitate analysis
filterNetworkssliderMax: used filter maximum value to facilitate analysis
smallBranchesTreatment: boolean - smallest circle used or not
originalGraph: a list of igraph
skeletonGraph: a list of igraph
shortestPaths: a data.table of shortest paths
networksCharacteristics: a data.table to store the skeleton graph characteristics
graphEvcent: an array to store Evcent
graphBetweenness: an array to store the graph betweenness
libVersion: version of the AFM library used to perform the analysis
updateProgress: a function to update a graphical user interface

Author(s)

M.Beauvais

[Package AFM version 2.0 Index]