require(RnavGraph)
require(RnavGraphImageData)
require(vegan)

data(frey)
## isomap data dimensionality reduction
#require(vegan) || stop("library vegan is needed for this demo.")
#frey2 <- t(frey)
dims <- 6 
#dise <- vegdist(frey2, method="euclidean")
#ord <- isomap(dise,k = 12, ndim= dims, fragmentedOK = TRUE)
data(ordfrey)

iso.frey <- data.frame(ordfrey$points)
## Images
## sample a few
sel <- seq(1,dim(frey)[2],3)
# 1:dim(frey)[2] #sample(1:dim(frey)[2],600, replace = FALSE)
ng.frey <- ng_image_array_gray('Brendan_Frey',frey[,sel],28,20, img_in_row = FALSE, rotate = 90)
ng.frey

V <- mapply(function(x){paste("i",x,sep="")},1:dims)
ng.iso.frey <- ng_data(name = "ISO_frey",
data = iso.frey[sel,],
shortnames = V)

#nav <- scagNav(ng.iso.frey,c("Clumpy","Outlying","Skewed","Monotonic", "Striated"),
#				images=ng.frey)
G <- completegraph(V)

LG <- linegraph(G)
LGnot <- complement(LG)
ng.LG <- ng_graph("3d frey", LG)
ng.LGnot <- ng_graph("4d frey", LGnot)

viz3d <- ng_2d(ng.iso.frey,ng.LG, images = ng.frey)
viz4d <- ng_2d(ng.iso.frey,ng.LGnot, images = ng.frey)

nav <- navGraph(ng.iso.frey,list(ng.LG,ng.LGnot),list(viz3d,viz4d))