read / write phylogenies with internal node names (JuliaPhylo#98)

read root name
dropped "#" from hybrid names
write internal names
read option: names -> namelabel

Author: cecileane

docs/src/man/expectedCFs.md

@@ -35,6 +35,7 @@ R"plot(0:1, 0:1, type='l', bty='L', lwd=0.3, col='#008080', xlab='quartet CF obs
 R"set.seed"(1234); # hide
 R"points(jitter($obsCF,amount=0.005),jitter($expCF,amount=0.005),col='#008080',bg='#00808090',pch=21)"; # hide
 R"dev.off()"; # hide
+nothing # hide
 ```
 To install ggplot2 if not installed already, do:
 `R"install.packages('ggplot2', dep=TRUE)"`

docs/src/man/snaq_plot.md

@@ -19,7 +19,7 @@ net3.loglik = 28.315067218909626
 ## Network Estimation
 
 SNaQ implements the statistical inference method in
-[Solís-Lemus and Ané 2016](http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1005896).
+[Solís-Lemus & Ané 2016](http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1005896).
 The procedure involves a numerical optimization of branch lengths and inheritance
 probabilities and a heuristic search in the space of phylogenetic networks.
 
@@ -47,6 +47,7 @@ R"svg(name('snaqplot_net0_1.svg'), width=4, height=3)" # hide
 R"par"(mar=[0,0,0,0]) # hide
 plot(net0, :R);
 R"dev.off()"; # hide
+nothing # hide
 ```
 ![net0_1](../assets/figures/snaqplot_net0_1.svg)
 
@@ -69,6 +70,7 @@ R"svg(name('snaqplot_net1_1.svg'), width=4, height=3)" # hide
 R"par"(mar=[0,0,0,0]) # hide
 plot(net1, :R, showGamma=true);
 R"dev.off()"; # hide
+nothing # hide
 ```
 ![net1_1](../assets/figures/snaqplot_net1_1.svg)
 
@@ -123,6 +125,7 @@ R"mtext"("hmax=2")           # add text annotation: title here
 plot(net3, :R, showGamma=true);
 R"mtext"("hmax=3")
 R"dev.off()"; # hide
+nothing # hide
 ```
 ![net23](../assets/figures/snaqplot_net23.svg)
 
@@ -272,6 +275,7 @@ R"svg(name('snaqplot_scores_heuristic.svg'), width=4, height=3)" # hide
 R"par"(mar=[2.5,2.5,.5,.5], mgp=[1.4,.4,0], tck=-0.02);  # hide
 R"plot"(scores, type="b", ylab="network score", xlab="hmax", col="blue");
 R"dev.off()"; # hide
+nothing # hide
 ```
 ![scores_heuristic](../assets/figures/snaqplot_scores_heuristic.svg)
 
@@ -306,6 +310,7 @@ R"svg(name('snaqplot_net1_2.svg'), width=4, height=3)" # starts image file
 R"par"(mar=[0,0,0,0]) # to reduce margins (no margins at all here)
 plot(net1, :R, showGamma=true, showEdgeNumber=true); # network is plotted & sent to file
 R"dev.off()"; # wrap up and save image file
+nothing # hide
 ```
 ![net1_2](../assets/figures/snaqplot_net1_2.svg)
 
@@ -322,6 +327,7 @@ R"svg(name('snaqplot_net1_3.svg'), width=4, height=3)" # hide
 R"par"(mar=[0,0,0,0]) # hide
 plot(net1, :R, showEdgeLength=true, minorHybridEdgeColor="tan")
 R"dev.off()"; # hide
+nothing # hide
 ```
 ![net1_3](../assets/figures/snaqplot_net1_3.svg)
 
@@ -342,6 +348,7 @@ R"par"(mar=[0,0,0,0]) # hide
 plot(net1,:R, tipOffset=0.5, showNodeNumber=true, edgeColor="tomato4",
      minorHybridEdgeColor="skyblue", majorHybridEdgeColor="tan");
 R"dev.off()"; # hide
+nothing # hide
 ```
 ![net1_4](../assets/figures/snaqplot_net1_4.svg)
 

src/auxiliary.jl

@@ -1210,44 +1210,59 @@ function switchHybridNode!(net::HybridNetwork, hybrid::Node, newHybrid::Node)
 end
 
 """
-`assignhybridnames!(net)`
+    assignhybridnames!(net)
 
-Assign names to hybrid nodes in the network `net`. Hybrid nodes with an empty `name` field ("")
-are modified with a name that does not conflict with other hybrid names in the network.
-The preferred name is "#H3" if the node number is 3 or -3, but an index other than 3 would be
-used if "#H3" were the name of another hybrid node already.
+Assign names to hybrid nodes in the network `net`.
+Hybrid nodes with an empty `name` field ("") are modified with a name that
+does not conflict with other hybrid names in the network. The preferred name
+is "H3" if the node number is 3 or -3, but an index other than 3 would be used
+if "H3" were the name of another node already.
 
 If two hybrid nodes have non-empty and equal names, the name of one of them is changed and
 re-assigned as described above (with a warning).
 """
 function assignhybridnames!(net::HybridNetwork)
-    hybnum = Int[]  # indices 'i' in hybrid names: #Hi
+    rx = r"^H(\d+)$"
+    # prep: collect indices 'i' of any tree nodes named like Hi
+    trenum = Int[]  # indices 'i' in tree node name, in case some are named Hi
+    for n in net.node
+        !n.hybrid || continue # do nothing if node n is hybrid
+        m = match(rx, n.name)
+        m == nothing || push!(trenum, parse(Int, m[1]))
+    end
     # first: go through *all* existing non-empty names
+    hybnum = Int[]  # indices 'i' in hybrid names: Hi
     for ih in 1:length(net.hybrid)
-        lab = net.hybrid[ih].name
+        hnode = net.hybrid[ih]
+        lab = hnode.name
         lab != "" || continue # do nothing if label is missing
         jh = findfirst(isequal(lab), [net.hybrid[j].name for j in 1:ih-1])
         if jh !== nothing # set repeated names to ""
-            @warn "hybrid nodes $(net.hybrid[ih].number) and $(net.hybrid[jh].number) have the same label: $lab. Will change the name of the former."
-            net.hybrid[ih].name = ""
-        else
-            m = match(r"^#H(\d+)$", lab)
-            if m != nothing # make full list of existing indices "i" in #Hi
-                push!(hybnum, parse(Int, m[1]))
+            @warn "hybrid nodes $(hnode.number) and $(net.hybrid[jh].number) have the same label: $lab. Will change the name of the former."
+            hnode.name = ""
+        else # fill in list of existing indices "i" in Hi
+            m = match(rx, lab)
+            m != nothing || continue # skip the rest if name is not of the form Hi
+            ind = parse(Int, m[1])
+            if ind in trenum
+                @warn "hybrid node $(hnode.number) had same label as a tree node: H$ind. Will change hybrid name."
+                hnode.name = ""
+            else
+                push!(hybnum, ind)
             end
         end
     end
-    # second: assign empty names to #Hi
+    # second: assign empty names to "Hi" for some i
     hnext = 1
     for ih in 1:length(net.hybrid)
         net.hybrid[ih].name == "" || continue # do nothing if non-empty label
         hnum = abs(net.hybrid[ih].number)
-        while in(hnum, hybnum)
+        while hnum in hybnum || hnum in trenum
             hnum = hnext  # not efficient, but rare
             hnext += 1    # and okay on small networks
         end
         push!(hybnum, hnum)
-        net.hybrid[ih].name = "#H$hnum"
+        net.hybrid[ih].name = "H$hnum"
     end
 end
 

src/descriptive.jl

@@ -153,7 +153,7 @@ function Base.show(io::IO, obj::HybridNetwork)
     try
         # par = writeTopology(obj,round=true) # but writeTopology changes the network, not good
         s = IOBuffer()
-        writeSubTree!(s, obj, false,true, true,3)
+        writeSubTree!(s, obj, false,true, true,3,false)
         par = String(take!(s))
     catch err
         println("ERROR with writeSubTree!:")