v2.0.0: compatibility with PhyloNetworks v0.17; output named tuple (b…

…reaking, #21 fix) (#26)

other breaking changes:

* removed plot method for models of two binary (correlated) traits
* the old method deprecation was removed

---------

Co-authored-by: Paul Bastide

.github/workflows/TagBot.yml

@@ -4,6 +4,22 @@ on:
     types:
       - created
   workflow_dispatch:
+    inputs:
+      lookback:
+        default: "3"
+permissions:
+  actions: read
+  checks: read
+  contents: write
+  deployments: read
+  issues: read
+  discussions: read
+  packages: read
+  pages: read
+  pull-requests: read
+  repository-projects: read
+  security-events: read
+  statuses: read
 jobs:
   TagBot:
     if: github.event_name == 'workflow_dispatch' || github.actor == 'JuliaTagBot'

Project.toml

@@ -1,7 +1,7 @@
 name = "PhyloPlots"
 uuid = "c0d5b6db-e3fc-52bc-a87d-1d050989ed3b"
 license = "MIT"
-version = "1.0.1"
+version = "2.0.0"
 
 [deps]
 DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
@@ -12,9 +12,9 @@ RCall = "6f49c342-dc21-5d91-9882-a32aef131414"
 
 [compat]
 DataFrames = "0.13, 0.14, 0.15, 0.16, 0.17, 0.18, 0.19, 0.20, 0.21, 0.22, 1.0"
-PhyloNetworks = "0.16, 0.17.0, 1.0.0" # extras to let PN build its documentation of new releases
+PhyloNetworks = "0.17"
 RCall = "0.11, 0.12, 0.13, 0.14"
-julia = "0.7, 1.0, 1.1, 1.2, 1.3, 1.4, 1.5, 1.6, 1.7"
+julia = "1.1, 1.2, 1.3, 1.4, 1.5, 1.6, 1.7"
 
 [extras]
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"

README.md

@@ -17,9 +17,11 @@ via [RCall](https://github.com/JuliaInterop/RCall.jl).
 
 ## examples
 
-in PhyloPlots' documentation [manual](https://juliaphylo.github.io/PhyloPlots.jl/stable/man/getting_started/), and  
-in [PhyloNetworks](http://juliaphylo.github.io/PhyloNetworks.jl/latest/)'s documentation, see
-- basic examples
-  [here](http://juliaphylo.github.io/PhyloNetworks.jl/latest/man/snaq_plot/#Network-Visualization-1)
-- examples to annotate edges
-  [here](http://juliaphylo.github.io/PhyloNetworks.jl/latest/man/bootstrap/#support-for-tree-edges)
+- in PhyloPlots' documentation [manual](https://juliaphylo.github.io/PhyloPlots.jl/stable/man/getting_started/)
+- in [PhyloNetworks](http://juliaphylo.github.io/PhyloNetworks.jl/latest/)'s documentation, see
+  * basic examples
+    [here](https://juliaphylo.github.io/PhyloNetworks.jl/dev/man/net_plot/#Network-Visualization)
+  * examples to annotate edges
+    [here](https://juliaphylo.github.io/PhyloNetworks.jl/dev/man/network_support/#support-for-tree-edges)
+- visualization with data in this
+  [tutorial](https://cecileane.github.io/networkPCM-workshop/topic6-visualization.html)

docs/Project.toml

@@ -1,6 +1,7 @@
 [deps]
 DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
+DocumenterInterLinks = "d12716ef-a0f6-4df4-a9f1-a5a34e75c656"
 PhyloNetworks = "33ad39ac-ed31-50eb-9b15-43d0656eaa72"
 PhyloPlots = "c0d5b6db-e3fc-52bc-a87d-1d050989ed3b"
 RCall = "6f49c342-dc21-5d91-9882-a32aef131414"

docs/make.jl

@@ -3,9 +3,16 @@ using Documenter
 using Pkg
 Pkg.add(PackageSpec(name="PhyloNetworks", rev="master"))
 
+using DocumenterInterLinks
+links = InterLinks(
+    "PhyloNetworks" => "https://juliaphylo.github.io/PhyloNetworks.jl/stable/objects.inv"
+)
 using PhyloNetworks
 using PhyloPlots
-DocMeta.setdocmeta!(PhyloPlots, :DocTestSetup, :(using PhyloPlots); recursive=true)
+# default loading of interlinked packages in all docstring examples
+DocMeta.setdocmeta!(PhyloPlots, :DocTestSetup,
+    :(using PhyloNetworks, PhyloPlots);
+    recursive=true)
 
 makedocs(
     sitename = "PhyloPlots.jl",

docs/src/man/adding_data.md

@@ -20,7 +20,7 @@ To add labels on edges (or nodes), we need to know their numbers. We can use the
 ```@example adding_data
 R"svg"(figname("adding_data1.svg"), width=6, height=3) # hide
 R"par"(mar=[.1,.1,.1,.1]); R"layout"([1 2]); # hide
-net = readTopology("(A,((B,#H1),((C)#H1, D)));") # hide
+net = readnewick("(A,((B,#H1),((C)#H1, D)));") # hide
 plot(net, showedgenumber=true);
 plot(net, showedgenumber=true, edgenumbercolor="red4");
 R"dev.off()" # hide
@@ -40,7 +40,7 @@ node), and the label that goes on it, like this:
 | 2      | "edge # 2" |
 
 After including the DataFrames package, we can define it as so:
-```@repl
+```@repl adding_data
 using DataFrames
 DataFrame(number=[1,2], label=["edge number 1","edge # 2"])
 ```
@@ -49,7 +49,7 @@ puts the text on the correct edges:
 ```@example adding_data
 R"svg"(figname("edge_labels_example.svg"), width=4, height=3) # hide
 R"par"(mar=[.1,.1,.1,.1]) # hide
-net = readTopology("(A,((B,#H1),(C,(D)#H1)));") # hide
+net = readnewick("(A,((B,#H1),(C,(D)#H1)));") # hide
 plot(net, edgelabel=DataFrame(number = [1,2],
                               label = ["edge number 1", "edge # 2"]),
           edgelabelcolor="orangered", edgecex=[0.9,1.1]);
@@ -63,12 +63,12 @@ nothing # hide
 We can use the return values of [`plot`](@ref) to get information on the coordinates of
 different elements of the plot. Using this, we can add any other information we want.
 
-The [`plot`](@ref) function returns the following tuple:
+The [`plot`](@ref) function returns the following named tuple:
 ```
-(xmin, xmax, ymin, ymax,
- node_x, node_y, node_yB, node_yE,
- edge_xB, edge_xE, edge_yB, edge_yE,
- nodedataframe, edgedataframe)
+(:xmin, :xmax, :ymin, :ymax,
+ :node_x,    :node_y,    :node_y_lo, :node_y_hi,
+ :edge_x_lo, :edge_x_hi, :edge_y_lo, :edge_y_hi,
+ :node_data, :edge_data)
 ```
 See the documentation for descriptions of these elements: [`plot`](@ref)
 
@@ -79,7 +79,7 @@ Here's example code that adds bars to denote clades in the margin:
 ```@example adding_data
 R"svg"(figname("side_bars.svg"), width=4, height=4) # hide
 R"par"(mar=[.1,.1,.1,.1]) # hide
-net = readTopology("(((((((1,2),3),4),5),(6,7)),(8,9)),10);");
+net = readnewick("(((((((t1,t2),t3),t4),t5),(t6,t7)),(t8,t9)),t10);");
 plot(net, xlim=(1,10))
 using RCall # to send any R command, to make further plot modifications
 R"segments"([9, 9, 9], [0.8, 7.8, 9.8], [9, 9, 9], [7.2, 9.2, 10.2])
@@ -97,7 +97,7 @@ because they contain the default range of the x axis; `xmin` and `xmax`.
 
 ```@example adding_data
 res = plot(net);
-res[1:2]
+res[[:xmin,:xmax]]
 ```
 
 Looking at `xmin` and `xmax` returned by default, we can see that the x
@@ -120,3 +120,17 @@ using RCall # add (install) the RCall package prior to 'using' it
 R"segments"([9, 9, 9], [0.8, 7.8, 9.8], [9, 9, 9], [7.2, 9.2, 10.2])
 R"text"([9.5, 9.5, 9.5], [4, 8.5, 10], ["C", "B", "A"])
 ```
+
+# Beyond
+
+To go beyond, we can access data on the node & edges to use them as we wish.
+We can access the coordinates of points & segments and more data like this:
+
+```@repl adding_data
+res[:node_x] # x coordinate. similarly try res[:node_y]
+hcat(res[:node_y_lo], res[:node_y_hi])
+DataFrame(edge_x_lo=res[:edge_x_lo], edge_x_hi=res[:edge_x_hi],
+          edge_y_lo=res[:edge_y_lo], edge_y_hi=res[:edge_y_hi])
+res[:node_data]
+res[:edge_data]
+```

docs/src/man/better_edges.md

@@ -15,7 +15,7 @@ but by switching it to `:majortree`, we can draw minor hybrid edges as diagonal
 ```@example better_edges
 R"svg"(figname("style_example.svg"), width=3, height=3) # hide
 R"par"(mar=[.1,.1,.1,.1]) # hide
-net = readTopology("(A,((B,#H1),(C,(D)#H1)));") # hide
+net = readnewick("(A,((B,#H1),(C,(D)#H1)));") # hide
 plot(net, style=:majortree);
 R"dev.off()" # hide
 nothing # hide
@@ -31,7 +31,7 @@ lines. For this, we'll use a network that has branch lengths:
 R"svg"(figname("edge_len_example.svg"), width=6, height=3) # hide
 R"par"(mar=[.1,.1,.1,.1]) # hide
 R"layout"([1 2]) # hide
-net = readTopology("(A:3.3,((B:1.5,#H1:0.5):1.5,((C:1)#H1:1.8,D:1.1):.2):0.3);")
+net = readnewick("(A:3.3,((B:1.5,#H1:0.5):1.5,((C:1)#H1:1.8,D:1.1):.2):0.3);")
 df = DataFrame(number=[-3,3], label=["N","H1"]); # hide
 plot(net, useedgelength=true, ylim = [-1, 5.5], nodelabel = df); # hide
 R"text"([3], [0], ["useedgelength=true"]) # hide
@@ -73,8 +73,8 @@ Time-inconsistent networks like these ones below might cause confusion:
 R"svg"(figname("edge_len_example2.svg"), width=6, height=3) # hide
 R"par"(mar=[.1,.1,.1,.1]) # hide
 R"layout"([1 2]) # hide
-net1 = readTopology("(A:3.3,((B:1.5,#H1:1.2):1.5,((C:1.8)#H1:1,D:1.1):.2):0.3);");
-net2 = readTopology("(A:3.3,((B:1.5,#H1:0.2):1.5,((C:1)#H1:1.8,D:1.1):.2):0.3);");
+net1 = readnewick("(A:3.3,((B:1.5,#H1:1.2):1.5,((C:1.8)#H1:1,D:1.1):.2):0.3);");
+net2 = readnewick("(A:3.3,((B:1.5,#H1:0.2):1.5,((C:1)#H1:1.8,D:1.1):.2):0.3);");
 plot(net1, useedgelength=true); # hide
 plot(net2, useedgelength=true); # hide
 R"dev.off()" # hide

docs/src/man/getting_started.md

@@ -16,14 +16,14 @@ using PhyloPlots
 ```
 Then read the topology
 ```@repl getting_started
-net = readTopology("(A,((B,#H1),(C,(D)#H1)));")
+net = readnewick("(A,((B,#H1),(C,(D)#H1)));")
 ```
 and call `plot`, as shown below.
 
 ```@example getting_started
 R"svg"(figname("gettingstarted.svg"), width=3, height=3) # hide
 R"par"(mar=[.1,.1,.1,.1]) # hide
-net = readTopology("(A,((B,#H1),(C,(D)#H1)));") # hide
+net = readnewick("(A,((B,#H1),(C,(D)#H1)));") # hide
 plot(net);
 R"dev.off()" # hide
 nothing # hide

docs/src/man/untangling_edges.md

@@ -20,7 +20,7 @@ whose child edges we should rotate.
 ```@example untangling
 R"svg"(figname("untangling1.svg"), width=3, height=3) # hide
 R"par"(mar=[.1,.1,.1,.1]) # hide
-net = readTopology("(A,((B,#H1),(C,(D)#H1)));") # hide
+net = readnewick("(A,((B,#H1),(C,(D)#H1)));") # hide
 plot(net, shownodenumber=true);
 R"dev.off()" # hide
 nothing # hide
@@ -32,7 +32,7 @@ As we can see, rotating edges around node `-5` will make for a prettier network.
 ```@example untangling
 R"svg"(figname("untangling2.svg"), width=3, height=3) # hide
 R"par"(mar=[.1,.1,.1,.1]) # hide
-net = readTopology("(A,((B,#H1),(C,(D)#H1)));") # hide
+net = readnewick("(A,((B,#H1),(C,(D)#H1)));") # hide
 rotate!(net, -5)
 plot(net)
 R"dev.off()" # hide

src/PhyloPlots.jl

@@ -18,7 +18,6 @@ export sexp
 
 include("phylonetworksPlots.jl")
 include("plotRCall.jl")
-include("substitutionmodels.jl")
 include("rexport.jl")
 
 end # of module