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JuliaPhylo · Mar 11, 2021 · 7275829 · 7275829 · cecileane · Mar 11, 2021
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commit 7275829
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Showing 6 changed files with 17 additions and 14 deletions.
diff --git a/.travis.yml b/.travis.yml
@@ -4,8 +4,7 @@ os:
   - linux
   - osx
 julia:
-  - 1.1
-  - 1.2
+  - 1.5
 
 notifications:
   email: false
@@ -38,7 +37,7 @@ coveralls: true
 jobs:
   include:
     - stage: "Documentation"
-      julia: 1.2
+      julia: 1.5
       os: linux
       script:
         - julia --project=docs/ -e 'using Pkg; Pkg.instantiate();

diff --git a/Project.toml b/Project.toml
@@ -1,7 +1,7 @@
 name = "PhyloPlots"
 uuid = "c0d5b6db-e3fc-52bc-a87d-1d050989ed3b"
 license = "MIT"
-version = "0.2.2"
+version = "0.2.3"
 
 [deps]
 ColorTypes = "3da002f7-5984-5a60-b8a6-cbb66c0b333f"
@@ -17,10 +17,10 @@ RCall = "6f49c342-dc21-5d91-9882-a32aef131414"
 ColorTypes = "0.7, 0.8, 0.9, 0.10"
 Colors = "0.9, 0.10, 0.11, 0.12"
 DataFrames = "0.13, 0.14, 0.15, 0.16, 0.17, 0.18, 0.19, 0.20, 0.21, 0.22"
-Gadfly = "1.0, 1.1, 1.2"
+Gadfly = "1.0, 1.1, 1.2, 1.3"
 PhyloNetworks = "0.9, 0.10, 0.11, 0.12"
 RCall = "0.11, 0.12, 0.13"
-julia = "0.7, 1.0, 1.1, 1.2, 1.3, 1.4"
+julia = "0.7, 1.0, 1.1, 1.2, 1.3, 1.4, 1.5"
 
 [extras]
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"

diff --git a/README.md b/README.md
@@ -1,6 +1,6 @@
 # PhyloPlots: to plot phylogenetic trees and networks
 
-[![Build Status](https://travis-ci.org/cecileane/PhyloPlots.jl.svg?branch=master)](https://travis-ci.org/cecileane/PhyloPlots.jl)
+[![Build Status](https://travis-ci.com/cecileane/PhyloPlots.jl.svg?branch=master)](https://travis-ci.com/cecileane/PhyloPlots.jl)
 [![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)
 

diff --git a/docs/Project.toml b/docs/Project.toml
@@ -7,4 +7,4 @@ DocumenterMarkdown = "997ab1e6-3595-5248-9280-8efb232c3433"
 # PhyloNetworks = "33ad39ac-ed31-50eb-9b15-43d0656eaa72"
 
 [compat]
-Documenter = "~0.24"
+Documenter = "~0.25"
diff --git a/src/phylonetworksPlots.jl b/src/phylonetworksPlots.jl
@@ -211,8 +211,10 @@ function prepareNodeDataFrame(net::HybridNetwork, nodeLabel::DataFrame,
         showNodeNumber::Bool, showIntNodeLabel::Bool, labelnodes::Bool,
         node_x::Array{Float64,1}, node_y::Array{Float64,1})
     nrows = (showNodeNumber || showIntNodeLabel || labelnodes ? net.numNodes : net.numTaxa)
-    ndf = DataFrame([String,String,String,Bool,Float64,Float64], # column types, column names, nrows
-           [Symbol("name"),Symbol("num"),Symbol("lab"),Symbol("lea"),Symbol("x"),Symbol("y")], nrows)
+    ndf = DataFrame(:name => Vector{String}(undef,nrows),
+        :num => Vector{String}(undef,nrows), :lab => Vector{String}(undef,nrows),
+        :lea => Vector{Bool}(  undef,nrows), :x => Vector{Float64}( undef,nrows),
+        :y => Vector{Float64}( undef,nrows), copycols=false)
     j=1
     for i=1:net.numNodes
     if net.node[i].leaf  || showNodeNumber || showIntNodeLabel || labelnodes
@@ -253,9 +255,11 @@ function prepareEdgeDataFrame(net::HybridNetwork, edgeLabel::DataFrame, mainTree
         edge_xB::Array{Float64,1}, edge_xE::Array{Float64,1},
         edge_yB::Array{Float64,1}, edge_yE::Array{Float64,1})
     nrows = net.numEdges - (mainTree ? net.numHybrids : 0)
-    edf = DataFrame([String,String,String,String,Bool,Bool,Float64,Float64],
-                  [Symbol("len"),Symbol("gam"),Symbol("num"),Symbol("lab"),
-                   Symbol("hyb"),Symbol("min"),Symbol("x"),Symbol("y")], nrows)
+    edf = DataFrame(:len => Vector{String}(undef,nrows),
+        :gam => Vector{String}(undef,nrows), :num => Vector{String}(undef,nrows),
+        :lab => Vector{String}(undef,nrows), :hyb => Vector{Bool}(undef,nrows),
+        :min => Vector{Bool}(  undef,nrows), :x => Vector{Float64}(undef,nrows),
+        :y  => Vector{Float64}(undef,nrows), copycols=false)
     labeledges = size(edgeLabel,1)>0
     if (labeledges && (size(edgeLabel,2)<2 ||
             !(nonmissingtype(eltype(edgeLabel[!,1])) <: Integer)))

diff --git a/src/plotRCall.jl b/src/plotRCall.jl
@@ -43,7 +43,7 @@ function plot(net::HybridNetwork, method::Symbol; useEdgeLength=false::Bool,
     edgeColor="black"::String,
     majorHybridEdgeColor="deepskyblue4"::String,
     minorHybridEdgeColor="deepskyblue"::String,
-    showEdgeNumber=false::Bool, showIntNodeLabel=true::Bool,
+    showEdgeNumber=false::Bool, showIntNodeLabel=false::Bool,
     edgeLabel=DataFrame()::DataFrame, nodeLabel=DataFrame()::DataFrame,
     xlim=Float64[]::Array{Float64,1}, ylim=Float64[]::Array{Float64,1},
     tipOffset=0.0::Float64, tipcex=1.0::Float64)