A S4 class to handle the networks calculation
AFMImageNetworksAnalysis()# S4 method for 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()
an AFMImageNetworksAnalysis Class
hash to transform coordinates to vertexId
the AFMImage after transformation before analysis
the AFMImage after transformation with the spotted circles
a data.table of identified circles
a data.table of edges
a data.table of correspon
a data.table of corresponsdance between intial node and fusioned node
a data.table of isolated nodes
used multiplier of heights to facilitate analysis
used filter minimum value to facilitate analysis
used filter maximum value to facilitate analysis
boolean - smallest circle used or not
a list of igraph
a list of igraph
a data.table of shortest path
a data.table to store the skeleton graph characteristics
a data.table to store the cluster number of each point
a data.table to summarize the data about holes
an array to store Evcent
an array to store the graph betweenness
version of the AFM library used to perform the analysis
vertexHashsizehash to transform coordinates to vertexId
binaryAFMImagethe AFMImage after transformation before analysis
binaryAFMImageWithCirclesthe AFMImage after transformation with the spotted circles
circlesTablea data.table of identified circles
edgesTablea data.table of edges
fusionedNodesCorrespondancea data.table of corresponsdance between intial node and fusioned node
fusionedNodesEdgesTablea data.table of nodes fusioned because of intersecting
isolatedNodesTablea data.table of isolated nodes
heightNetworkssliderused multiplier of heights to facilitate analysis
filterNetworkssliderMinused filter minimum value to facilitate analysis
filterNetworkssliderMaxused filter maximum value to facilitate analysis
smallBranchesTreatmentboolean - smallest circle used or not
originalGrapha list of igraph
skeletonGrapha list of igraph
shortestPathsa data.table of shortest paths
networksCharacteristicsa data.table to store the skeleton graph characteristics
graphEvcentan array to store Evcent
graphBetweennessan array to store the graph betweenness
libVersionversion of the AFM library used to perform the analysis
updateProgressa function to update a graphical user interface