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 |
skeletonGraph |
a list of |
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