fix: remove extra dot on lower right corner (#18)

JuliaPhylo · May 6, 2022 · 270808c · 270808c
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diff --git a/README.md b/README.md
@@ -1,7 +1,8 @@
 # PhyloPlots: to plot phylogenetic trees and networks
 
+[![Stable](https://img.shields.io/badge/docs-stable-blue.svg)](https://cecileane.github.io/PhyloPlots.jl/stable)
+[![Dev](https://img.shields.io/badge/docs-dev-blue.svg)](https://cecileane.github.io/PhyloPlots.jl/dev)
 [![Build status](https://github.com/cecileane/PhyloPlots.jl/workflows/CI/badge.svg?branch=master)](https://github.com/cecileane/PhyloPlots.jl/actions/workflows/ci.yml)
-[![Coverage Status](https://coveralls.io/repos/cecileane/PhyloPlots.jl/badge.svg?branch=master&service=github)](https://coveralls.io/github/cecileane/PhyloPlots.jl?branch=master)
 [![codecov.io](http://codecov.io/github/cecileane/PhyloPlots.jl/coverage.svg?branch=master)](http://codecov.io/github/cecileane/PhyloPlots.jl?branch=master)
 
 ## overview
@@ -12,12 +13,10 @@ using plotting back-ends like [Gadfly](http://gadflyjl.org/stable/),
 and through [R](https://www.r-project.org)
 via [RCall](https://github.com/JuliaInterop/RCall.jl).
 
-[![](https://img.shields.io/badge/docs-stable-blue.svg)](https://cecileane.github.io/PhyloPlots.jl/stable)
-[![](https://img.shields.io/badge/docs-dev-blue.svg)](https://cecileane.github.io/PhyloPlots.jl/dev)
-
 ## examples
 
-in the documentation for [PhyloNetworks](http://crsl4.github.io/PhyloNetworks.jl/latest/), see
+in PhyloPlots' documentation [manual](https://cecileane.github.io/PhyloPlots.jl/stable/man/getting_started/), and  
+in [PhyloNetworks](http://crsl4.github.io/PhyloNetworks.jl/latest/)'s documentation, see
 - basic examples
   [here](http://crsl4.github.io/PhyloNetworks.jl/latest/man/snaq_plot/#Network-Visualization-1)
 - examples to annotate edges

diff --git a/src/phylonetworksPlots.jl b/src/phylonetworksPlots.jl
@@ -76,7 +76,10 @@ function getEdgeNodeCoordinates(net::HybridNetwork, useEdgeLength::Bool, useSimp
         cur_edge = pop!(cladewise_queue); # deliberate choice over shift! for cladewise order
         # increment spacing and add to node_y if leaf
         if getChild(cur_edge).leaf
-            node_y[findfirst(x->x===getChild(cur_edge), net.node)] = nexty
+            ni = findfirst(x->x===getChild(cur_edge), net.node)
+            node_y[ni]  = nexty
+            node_yB[ni] = nexty
+            node_yE[ni] = nexty
             nexty -= 1
         end
 

diff --git a/test/test_phylonetworkPlots.jl b/test/test_phylonetworkPlots.jl
@@ -13,8 +13,8 @@
     [1.0, 2.0, 3.0, 2.5, 4.0, 5.0, 5.0, 4.5, 3.5],
     [3.5, 3.5, 2.5, 3.5, 3.5, 3.0, 2.5, 1.5, 1.0],
     [1.0, 2.0, 2.5, 4.0, 5.0, 5.0, 4.5, 3.5, 2.25],
-    [0.0, 0.0, 2.0, 0.0, 0.0, 5.0, 4.0, 2.5, 1.0],
-    [0.0, 0.0, 3.0, 0.0, 0.0, 5.0, 5.0, 4.5, 3.5],
+    [1.0, 2.0, 2.0, 4.0, 5.0, 5.0, 4.0, 2.5, 1.0],
+    [1.0, 2.0, 3.0, 4.0, 5.0, 5.0, 5.0, 4.5, 3.5],
     [3.0], [3.0], [3.0], [5.0], 1.0, 3.5, 1.0, 5.0)
   @test PhyloPlots.getEdgeNodeCoordinates(net, true, true) == (
     [1.0, 2.5, 2.5, 1.5, 2.5, 3.0, 2.5, 1.5, 1.0],
@@ -23,8 +23,8 @@
     [1.0, 2.0, 2.0, 2.0, 3.0, 4.0, 4.0, 3.5, 2.75],
     [3.5, 3.5, 2.5, 3.5, 3.5, 3.0, 2.5, 1.5, 1.0],
     [1.0, 2.0, 2.0, 3.0, 4.0, 4.0, 3.5, 2.75, 1.875],
-    [0.0, 0.0, 2.0, 0.0, 0.0, 4.0, 3.0, 2.0, 1.0],
-    [0.0, 0.0, 2.0, 0.0, 0.0, 4.0, 4.0, 3.5, 2.75],
+    [1.0, 2.0, 2.0, 3.0, 4.0, 4.0, 3.0, 2.0, 1.0],
+    [1.0, 2.0, 2.0, 3.0, 4.0, 4.0, 4.0, 3.5, 2.75],
     [2.5], [3.0], [2.0], [4.0], 1.0, 3.5, 1.0, 4)
   @test PhyloPlots.getEdgeNodeCoordinates(net, false, true) == (
     [1.0, 3.0, 3.0, 2.0, 3.0, 4.0, 3.0, 2.0, 1.0],
@@ -33,8 +33,8 @@
     [1.0, 2.0, 2.0, 2.0, 3.0, 4.0, 4.0, 3.5, 2.75],
     [5.0, 5.0, 3.0, 5.0, 5.0, 4.0, 3.0, 2.0, 1.0],
     [1.0, 2.0, 2.0, 3.0, 4.0, 4.0, 3.5, 2.75, 1.875],
-    [0.0, 0.0, 2.0, 0.0, 0.0, 4.0, 3.0, 2.0, 1.0],
-    [0.0, 0.0, 2.0, 0.0, 0.0, 4.0, 4.0, 3.5, 2.75],
+    [1.0, 2.0, 2.0, 3.0, 4.0, 4.0, 3.0, 2.0, 1.0],
+    [1.0, 2.0, 2.0, 3.0, 4.0, 4.0, 4.0, 3.5, 2.75],
     [3.0], [4.0], [2.0], [4.0], 1.0, 5.0, 1.0, 4)
   dat = DataFrame(node=[-5,-3,-4,5,100],bs=["90","95","99","mytip","bogus"],edge=[8,9,4,6,200]);
   @test_logs (:warn, "Some node numbers in the nodeLabel data frame are not found in the network:\n 100") PhyloPlots.checkNodeDataFrame(net, dat);
@@ -76,8 +76,8 @@
     [5.0, 4.0, 1.0, 2.0, 3.0, 4.0, 3.0, 5.0, 6.0, 5.5, 4.25],
     [6.0, 5.0, 4.0, 6.0, 6.0, 3.0, 6.0, 4.0, 2.0, 1.0],
     [5.0, 5.0, 4.0, 2.0, 3.0, 3.0, 6.0, 5.5, 4.25, 2.625],
-    [0.0, 5.0, 4.0, 0.0, 0.0, 2.0, 0.0, 5.0, 3.0, 1.0],
-    [0.0, 5.0, 4.0, 0.0, 0.0, 4.0, 0.0, 6.0, 5.5, 4.25],
+    [5.0, 5.0, 4.0, 2.0, 3.0, 2.0, 6.0, 5.0, 3.0, 1.0],
+    [5.0, 5.0, 4.0, 2.0, 3.0, 4.0, 6.0, 6.0, 5.5, 4.25],
     [5.0, 4.0], [5.0, 4.0], [4.0, 1.0], [5.0, 4.0],
     1.0, 6.0, 1.0, 6.0)
   net = readTopology("((((B)#H1:::0.2)#H2,((D,C,#H2)S1,(#H1,A)S2)S3)S4);")
@@ -89,8 +89,8 @@
     [5.0, 1.0, 1.0, 2.0, 3.0, 4.0, 3.0, 5.0, 6.0, 5.5, 4.25],
     [6.0, 5.0, 4.0, 6.0, 6.0, 3.0, 6.0, 4.0, 2.0, 1.0],
     [5.0, 5.0, 1.0, 2.0, 3.0, 3.0, 6.0, 5.5, 4.25, 2.625],
-    [0.0, 5.0, 1.0, 0.0, 0.0, 2.0, 0.0, 5.0, 3.0, 1.0],
-    [0.0, 5.0, 1.0, 0.0, 0.0, 4.0, 0.0, 6.0, 5.5, 4.25],
+    [5.0, 5.0, 1.0, 2.0, 3.0, 2.0, 6.0, 5.0, 3.0, 1.0],
+    [5.0, 5.0, 1.0, 2.0, 3.0, 4.0, 6.0, 6.0, 5.5, 4.25],
     [5.0, 4.0], [5.0, 4.0], [1.0, 4.0], [5.0, 1.0],
     1.0, 6.0, 1.0, 6.0)
 end