Merge pull request #19 from EcoJulia/force-dir

🙂 simplify the FD code

docs/make.jl

@@ -4,8 +4,18 @@ using Documenter, EcologicalNetworksPlots
 
 const pages = [
     "Index" => "index.md",
-    "Examples" => "examples.md",
-    "Reference" => "library.md"
+    "Layouts" => [
+        "Introduction" => "layouts/initial.md",
+        "Circular" => "layouts/circular.md",
+        "Bipartite" => "layouts/bipartite.md",
+        "Force-directed" => "layouts/forcedirected.md",
+        "Unravel" => "layouts/unravelled.md"
+    ],
+    "Advanced topics" => [
+        "Nodes attributes" => "advanced/attributes.md",
+        "Networks subsets" => "advanced/subsets.md",
+    ]
+    # TODO add plotting, heatmap, advanced uses
 ]
 
 makedocs(
@@ -15,6 +25,6 @@ makedocs(
     )
 
 deploydocs(
-    repo = "github.com/PoisotLab/EcologicalNetworksPlots.jl.git",
+    repo = "github.com/EcoJulia/EcologicalNetworksPlots.jl.git",
     push_preview = true
 )

docs/src/advanced/attributes.md

@@ -0,0 +1,39 @@
+## Node color
+
+```@setup default
+using EcologicalNetworks
+using EcologicalNetworksPlots
+using Plots
+```
+
+```@example default
+Unes = web_of_life("M_SD_033")
+I = initial(BipartiteInitialLayout, Unes)
+position!(NestedBipartiteLayout(0.4), I, Unes)
+plot(I, Unes, aspectratio=1)
+scatter!(I, Unes, bipartite=true, nodefill=degree(Unes), c=:cividis)
+```
+
+## Node size
+
+The size of the nodes can be changed using the `nodesize` argument, which is a
+dictionary mapping species to values. These values are scaled when making the
+figures. Note that in this example we also label the number of the node.
+
+```@example default
+Unes = web_of_life("M_SD_033")
+I = initial(BipartiteInitialLayout, Unes)
+position!(NestedBipartiteLayout(0.4), I, Unes)
+plot(I, Unes, aspectratio=1)
+scatter!(I, Unes, bipartite=true, nodesize=degree(Unes))
+```
+
+## Node annotations
+
+```@example default
+Unes = web_of_life("M_SD_033")
+I = initial(BipartiteInitialLayout, Unes)
+position!(NestedBipartiteLayout(0.4), I, Unes)
+plot(I, Unes, aspectratio=1)
+scatter!(I, Unes, bipartite=true, series_annotations = string.(1:richness(Unes)))
+```

docs/src/advanced/subsets.md

@@ -0,0 +1,23 @@
+```@setup default
+using EcologicalNetworks
+using EcologicalNetworksPlots
+using Plots
+```
+
+One important feature of the package is that the layout can contain *more* nodes
+than the network. For example, we can use this to our advantage, to represent
+species with a degree larger than 3 in red:
+
+```@example default
+Umod = web_of_life("M_PA_003")
+I = initial(RandomInitialLayout, Umod)
+for step in 1:4000
+  position!(ForceDirectedLayout(2.5, 0.4), I, Umod)
+end
+plot(I, Umod, aspectratio=1)
+scatter!(I, Umod)
+N = convert(AbstractUnipartiteNetwork, convert(BinaryNetwork, Umod))
+core3 = collect(keys(filter(p -> p.second == 3, degree(N))))
+plot!(I, N[core3], lc=:red)
+scatter!(I, N[core3], mc=:red)
+```

docs/src/index.md

@@ -10,14 +10,20 @@ The second option requires to set a layout, of which there are multiple types
 according to the type of network, the type of layout, and the information to
 emphasize. Applying a layout consists of a call to `initial`, followed by one or
 more calls to `position!`. The *nodes* in the network are represented using
-`scatter`, and the *links* using `plot`.
-
-Probabilistic networks have link *probability* denoted as transparency, and
-quantitative network have link *strength* represented as width.
+`scatter`, and the *links* using `plot`. Probabilistic networks have link
+*probability* denoted as transparency, and quantitative network have link
+*strength* represented as width.
 
 Both the fill and color of the nodes can be changed, using the `nodefill`
 and `nodesize` arguments -- these must be dictionaries mapping *all nodes* in
 the network to a single numerical value, and they affect the `markerfill` and
 `markerz` value of `Plots`, respectively. Note that by default, `frametype` is
 `:none` and `legend` is `false`, but this can be changed. It is particularly
 important to change it for `UnravelledLayout`, for example.
+
+An important point, which can be used to create complex visualisations, is that
+you can call the `scatter` and `plot` functions on dictionaries of positions
+that have *more* points that are in the network. This can, among other things,
+allow you to use different colormaps for the degree of different nodes, or color
+different sub-graphs in the network. There are a few example of these uses in
+the documentation.

docs/src/layouts/bipartite.md

@@ -0,0 +1,22 @@
+## Layouts
+
+```@docs
+BipartiteInitialLayout
+NestedBipartiteLayout
+```
+
+```@setup default
+using EcologicalNetworks
+using EcologicalNetworksPlots
+using Plots
+```
+
+## Example
+
+```@example default
+Unes = web_of_life("M_SD_033")
+I = initial(BipartiteInitialLayout, Unes)
+position!(NestedBipartiteLayout(0.4), I, Unes)
+plot(I, Unes, aspectratio=1)
+scatter!(I, Unes, bipartite=true)
+```

docs/src/layouts/circular.md

@@ -0,0 +1,22 @@
+## Layouts
+
+```@docs
+CircularInitialLayout
+CircularLayout
+```
+
+```@setup default
+using EcologicalNetworks
+using EcologicalNetworksPlots
+using Plots
+```
+
+## Example
+
+```@example default
+Unes = web_of_life("M_SD_033")
+I = initial(CircularInitialLayout, Unes)
+position!(CircularLayout(), I, Unes)
+plot(I, Unes, aspectratio=1)
+scatter!(I, Unes, bipartite=true)
+```