Graph, ToolTip, and Labeled: How to make a swanky graph

Question

Problem

I do not understand Mathematica's Documentation for Labeled, VertexLabels, VertexRenderingFunction, etc

I want to make a Graph that has Tooltip enabled for verticies and edges, has PopupWindow enabled for the verticies, has different colors for edges of different type, different colors for specific verticies, and smaller arrows, etc.

Example

I have a list of index pairs, e.g.

indexList = {
{1,3},{1,4},{1,5},
{4,2},{4,1},
{5,2}
};

Just for purpose of this example lets say I have a list with labels for my verticies and edges

vertexLabels = {"a","b","c","d","e"};
edgeLabels = {"e1","e2","e3","e4","e5","e6"};

Convert index pairs to directed edges

directedEdges = Table[indexList[[i]][[1]] \[DirectedEdge] indexList[[i]][[2]],{i,1,Length[indexList]}];

Apply Tooltip to directed edges

directedEdgesTooltip = Table[Tooltip[directedEdges[[i]], edgeLabels[[i]]],{i,1,Length[directedEdges]}];

But supposedily one can use Labeled

directedEdgesLabeled = Table[Labeled[directedEdges[[i]], edgeLabels[[i]],Tooltip],{i,1,Length[directedEdges]}];

Calling Graph on this works-ish Graph[directedEdgesLabeled]

But that isn't how it should work. Supposedily I should call

Graph[directedEdges,EdgeLabels -> directedEdgesLabeled]

But that doesn't work. As you'll see this goes on for Verticies too.

Apply Tooltip to Verticies

verticiesLabeled = Table[Labeled[Range[5][[i]], vertexLabels[[i]],Tooltip],{i,1,Length[Range[5]]}];

So lets try again

Graph[directedEdges, VertexLabels -> verticiesLabeled]

Oh darn... that doesn't work.

What about using Tooltip on the directedEdges? Well that works, if you only want the vertex labeled.

Note

Nesting Labeled does not work

Labeled[Labeled[1, "a", Tooltip] \[DirectedEdge] Labeled[2, "b", Tooltip], "e1", Tooltip]

Question

So please someone tell me how to do this. We haven't even got into adding PopupWindow (which I have tried a myraid of methods for).

Answer 1

Answer to getting Labeled Edges and Verticies

1.) Do not use Labeled, use Placed. See below:

makeEdgeLabels[directedEdges_] := 
 Table[directedEdges[[i]] -> 
   Placed[getEdgeLabel[directedEdges[[i]]], Tooltip], {i, 1, 
   Length[directedEdges]}]

makeVertexLabels[indexList_] := Module[
  {iL = DeleteDuplicates[Flatten[indexList]]},
  Return[
   Table[iL[[i]] -> Placed[proteinNames[[iL[[i]]]], Tooltip], {i, 1, 
     Length[iL]}]
   ]
  ]


Graph[directedEdges,EdgesLabels-> makeEdgeLabels[directedEdges],VertexLabels->makeVertexLabels[directedEdges]]