@@ -112,8 +112,9 @@ layout.arc = function (g, target, query)

   target = target[target %in% query]

   V(g)$type = "bridge"

-  V(g)[name %in% query]$type = "query"

-  V(g)[name %in% target]$type = "target"

+  all_name=V(g)$name # could be V(g)[ name %in% query ] but want to avoid "note's" in R CMD check.

+  V(g)[all_name %in% query]$type = "query"

+  V(g)[all_name %in% target]$type = "target"

   g_con = g

   n_left = character()

@@ -123,9 +124,11 @@ layout.arc = function (g, target, query)

     n_left = setdiff(V(g)$name,V(g_con)$name)

   }

-  set = list(target = target, bridge=V(g_con)[type == "bridge"]$name, query1 = character(), query2 = character(), query3 = character(), left=n_left)

-  for(q in V(g_con)[type == "query"]$name) {

-    sp = get.all.shortest.paths(g_con,from=V(g_con)[q],to=V(g_con)[name %in% target])

+  all_type=V(g_con)$type

+  all_name=V(g_con)$name

+  set = list(target = target, bridge=V(g_con)[all_type == "bridge"]$name, query1 = character(), query2 = character(), query3 = character(), left=n_left)

+  for(q in V(g_con)[all_type == "query"]$name) {

+    sp = get.all.shortest.paths(g_con,from=V(g_con)[q],to=V(g_con)[all_name %in% target])

     #print(sp)

     sp_min = min(sapply(sp$res,length))

     #print(sp_min)

@@ -126,9 +126,9 @@ layout.arc = function (g, target, query)

   set = list(target = target, bridge=V(g_con)[type == "bridge"]$name, query1 = character(), query2 = character(), query3 = character(), left=n_left)

   for(q in V(g_con)[type == "query"]$name) {

     sp = get.all.shortest.paths(g_con,from=V(g_con)[q],to=V(g_con)[name %in% target])

-    print(sp)

+    #print(sp)

     sp_min = min(sapply(sp$res,length))

-    print(sp_min)

+    #print(sp_min)

     if(sp_min == 2) {

       set$query1 = c(set$query1, V(g_con)[q]$name)

     }

@@ -99,3 +99,62 @@ getConcentricList = function(g, t, e, max.size = 60, order.by = "label") {

 	}

 	res

 }

+

+layout.arc = function (g, target, query)

+{

+  n = vcount(g)

+  if(! all(target %in% V(g)$name)) {

+    warning("some targets not in graph, removing them.")

+    target=target[target %in% V(g)$name]

+  }

+  

+  #

+  target = target[target %in% query]

+  

+  V(g)$type = "bridge"

+  V(g)[name %in% query]$type = "query"

+  V(g)[name %in% target]$type = "target"

+  

+  g_con = g

+  n_left = character()

+  

+  if(! is.connected(g)) {

+    g_con = getLargestComp(g)

+    n_left = setdiff(V(g)$name,V(g_con)$name)

+  }

+  

+  set = list(target = target, bridge=V(g_con)[type == "bridge"]$name, query1 = character(), query2 = character(), query3 = character(), left=n_left)

+  for(q in V(g_con)[type == "query"]$name) {

+    sp = get.all.shortest.paths(g_con,from=V(g_con)[q],to=V(g_con)[name %in% target])

+    print(sp)

+    sp_min = min(sapply(sp$res,length))

+    print(sp_min)

+    if(sp_min == 2) {

+      set$query1 = c(set$query1, V(g_con)[q]$name)

+    }

+    else set$query2 = c(set$query2, V(g_con)[q]$name)

+  }

+  

+  set = lapply(set,function(s) {

+    ns = V(g)[s]$label

+    s[order(ns,decreasing=TRUE)]

+  })

+  

+  x0 = c(left=-2,query1=-1,target=0,bridge=1,query2=2)

+  y0 = sapply(set,function(x){

+    -1 * floor(length(x)/2)

+  })

+  

+  res = matrix(NA, nrow = n, ncol = 2)

+  all_n = unlist(set)

+  for(my_n in all_n) {

+    k = which(V(g)$name == my_n)

+    my_type = names(set)[sapply(set,function(x) my_n %in% x)]

+    x1 = x0[my_type]

+    y1 = y0[my_type]

+    y0[my_type] = y0[my_type] + 1

+    res[k,1] = x1

+    res[k,2] = y1

+  }

+  res

+}

\ No newline at end of file

new file mode 100644

@@ -0,0 +1,101 @@

+.getCoordinates = function(x, r) {

+	l = length(x)

+	d = 360/l

+	c1 = seq(0, 360, d)

+	c1 = c1[1:(length(c1)-1)]

+	tmp = t(sapply(c1, function(cc) c(cos(cc*pi/180)*r, sin(cc*pi/180)*r)))

+	rownames(tmp) = x

+	tmp

+}

+

+.checkValid = function(x) {

+	if(any(table(x) > 1)) FALSE else TRUE

+}

+

+# TODO: make layout independent the $name $label (i.e. based on indexes.)

+layout.concentric = function (g, concentric = NULL, radius = NULL, order.by) 

+{

+	if(is.null(concentric))

+    concentric = list(V(g)$name)

+

+	all_c = unlist(concentric, use.names = FALSE)

+	

+  if (!.checkValid(all_c))

+	  stop("Duplicated nodes in layers!")

+	

+	if (!.checkValid(radius)) 

+	  stop("Duplicated radius in layers!")

+	

+	all_n = V(g)$name

+	sel_other = all_n[ ! all_n %in% all_c ]

+	

+	if(length(sel_other) > 0)

+	  concentric[[length(concentric)+1]] = sel_other

+    

+	if(is.null(radius)) {

+		radius = seq(0, 1, 1/(length(concentric)))

+		if(length(concentric[[1]]) == 1)

+			radius = radius[-length(radius)]

+		else

+			radius = radius[-1]

+	}

+	

+	if( ! missing(order.by) )

+		order.values = lapply(order.by, function(b) get.vertex.attribute(g, b))

+		

+	res = matrix(NA, nrow = length(all_n), ncol = 2)

+	for(k in 1:length(concentric)) {

+		r = radius[k]

+		l = concentric[[k]]

+    

+		i = which(V(g)$name %in% l) - 1

+		i_o = i

+		if (!missing(order.by)) {

+			ob = lapply(order.values, function(v) v[i + 1])

+			ord = do.call(order, ob)

+			i_o = i_o[ord]

+		}

+		res[i_o+1, ] = .getCoordinates(i_o, r)

+

+	}

+	res

+}

+

+getConcentricList = function(g, t, e, max.size = 60, order.by = "label") {

+	sel.all = V(g)$name

+	

+	# filter out not in graph.

+	t = t[t %in% sel.all]

+	e = e[e %in% sel.all]

+	

+	sel.e = V(g)[ e ]$name

+	sel.t = V(g)[ t ]$name

+	sel.t = sel.t[sel.t %in% sel.e ] # choose only target that are enriched.

+	sel.e = sel.e[! sel.e %in% sel.t ]

+	

+	sel.b = sel.all[! sel.all %in% c(sel.t, sel.e) ]

+	

+	tmp = list(sel.t, sel.b, sel.e)

+

+  if(!is.null(order.by)) {

+    tmp = lapply(tmp, function(l) {

+      l[order(get.vertex.attribute(g, order.by, V(g)[ l ]))]

+    })

+  }

+

+	res = list()

+	for(k in 1:length(tmp)) {

+		r = tmp[[k]]

+    if(length(r)>max.size) {

+      s = ceiling(length(r)/max.size)

+      #r1 = split(r,rep(1:s, s,length.out = length(r)))

+      v = rep(1:s, each = ceiling(length(r)/s))

+      v = v[1:length(r)]

+      r1 = split(r,v)

+      for(kk in r1) {

+        res[[length(res)+1]] = kk

+      } 

+    }	else res[[length(res)+1]] = r

+	}

+	res

+}