Change rgl.* functions to *3d, update igraph pckg.

.gitignore

@@ -5,3 +5,5 @@
 inst/doc
 doc
 Meta
+/doc/
+/Meta/

R/mully_visualization.R

@@ -168,23 +168,23 @@ plot3d <- function(g, layers = TRUE,
   if(length(V(g))==0){
     stop("This mully Graph has no nodes.")
   }
-  open3d()
-  bg3d(
+  rgl::open3d()
+  rgl::bg3d(
     sphere = TRUE,
     color = c("white", "blue"),
     lit = FALSE,
     back = "lines"
   )
   gps = getMarkGroups(g)
-
+  nLayers=dim(g$layers)[1]
   colrs = randomColor(count = g$iLayer)
 
   assignedColors=V(g)$color
   usedCols = unique(assignedColors)
   if (is.null(V(g)$color))
     V(g)$color = NA
 
-  for (i in 1:dim(g$layers)[1]) {
+  for (i in 1:nLayers) {
     idLayer=as.integer(g$layers$ID[i])
     nodesid=which(V(g)$n == idLayer)
     if(is.null(nodesid) || length(nodesid)==0)
@@ -277,7 +277,7 @@ plot3d <- function(g, layers = TRUE,
         coord = t(as.matrix(layout1[temp, ]))
       else
         coord = as.matrix(layout1[temp:(temp + nNodes - 1), ])
-      plane = suppressWarnings(get3DPlane(coord, dim(g$layers)[1],nNodes))
+      plane = get3DPlane(coord, nLayers,nNodes)
       planes3d(
         0,
         b = plane[2],
@@ -287,13 +287,12 @@ plot3d <- function(g, layers = TRUE,
         alpha = 0.2
       )
       #Add layers' names
-      text3d(
+      rgl::text3d(
         x = -max(abs(layout[, 1]))-1,
         y = coord[1, 2],
         z = min(abs(layout[, 3])) - 2,
         texts = paste0(nameLayer," Layer",sep=""),
         color = clrs[iColr],
-        alpha = 1
       )
       iColr=iColr+1
       temp = temp + nNodes

mully.Rcheck/00_pkg_src/mully/R/mully_visualization.R

@@ -162,8 +162,7 @@ plot3d <- function(g, layers = TRUE,
   if(length(V(g))==0){
     stop("This mully Graph has no nodes.")
   }
-  rgl.open()
-  rgl.bg(
+  rgl::bg3d(
     sphere = TRUE,
     color = c("white", "blue"),
     lit = FALSE,
@@ -225,7 +224,7 @@ plot3d <- function(g, layers = TRUE,
 
   layout = get3DLayout(g,vertex.plac)
 
-  open3d()
+  rgl::open3d()
   igraph::rglplot(
     g,
     vertex.color = V(g)$color,
@@ -262,7 +261,7 @@ plot3d <- function(g, layers = TRUE,
       else
         coord = as.matrix(layout1[temp:(temp + nNodes - 1), ])
       plane = suppressWarnings(get3DPlane(coord, dim(g$layers)[1],nNodes))
-      rgl.planes(
+      rgl::planes3d(
         0,
         b = plane[2],
         0,
@@ -271,7 +270,7 @@ plot3d <- function(g, layers = TRUE,
         alpha = 0.2
       )
       #Add layers' names
-      text3d(
+      rgl::texts3d(
         x = -max(abs(layout[, 1]))-1,
         y = coord[1, 2],
         z = min(abs(layout[, 3])) - 2,