In Albluca/rpgraph: r interface to VDAOEngine to build elastic principal graphs

This vignette present a few simple examples describing the usage of the package RPrinGraph. For a more deailed description of the package and for various instruction on installation refer to a different vignette.

An essential overview of Pircipal elastic circles

rpgraph prerequisite and instakllation

dyn.load('/Library/Java/JavaVirtualMachines/jdk1.7.0_79.jdk/Contents/Home/jre/lib/server/libjvm.dylib')

This may be necessary for Mac systems:

Workaround for common problems

Example 1 - Circle

library(rpcurve)

Data <- simple_circle

Results <- computeElasticPrincipalGraph(Data = Data, NumNodes = 40, Method = 'CircleConfiguration')

plotMSDEnergyPlot(Results, Main = "Pincipal Circle", Cex.Main = 1)

accuracyComplexityPlot(Results, Main = "Pincipal Circle", Cex.Main = 1, Mode = 5)

accuracyComplexityPlot(Results, Main = "Pincipal Circle", Cex.Main = 1, Xlims = c(.9, 1))

accuracyComplexityPlot(Results, Main = "Pincipal Circle", Cex.Main = 1, Xlims = c(.97, .98))

plotData2D(Data = simple_circle, PrintGraph = Results,
           GroupsLab = rep(1, nrow(simple_circle)), Xlab = "Dimension 1", Ylab = "Dimension 2")

plotData2D(Data = simple_circle, PrintGraph = Results, Plot.ly = TRUE,
           GroupsLab = rep(1, nrow(simple_circle)), Xlab = "Dimension 1", Ylab = "Dimension 2")

plotData3D(Data = simple_circle, PrintGraph = Results, Plot.ly = TRUE,
           GroupsLab = rep(1, nrow(simple_circle)))

library("rgl")
open3d()
plotData3D(Data = simple_circle, PrintGraph = Results, Plot.ly = FALSE,
           GroupsLab = rep(1, nrow(simple_circle)), NodeSizeMult = 0.05)

Net <- ConstructGraph(Results = Results, DirectionMat = NULL, Thr = 0.05)
TaxonList <- getTaxonMap(Results = Results, Data = Data)

InfoData <- plotPieNet(Results = Results, Data = simple_circle, Categories = rep(1, nrow(simple_circle)),
           Graph = Net, TaxonList = TaxonList, LayOut = 'circle', Main = "Pincipal Circle")