AFMImageNetworksAnalysis-class: AFM image networks analysis class

In AFM: Atomic Force Microscope Image Analysis

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

AFM documentation built on Oct. 23, 2020, 5:23 p.m.