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]