Project.toml; new indexing rules from DataFrames v0.19

fix R install on Travis

Author: cecileane

.gitignore

@@ -3,3 +3,4 @@
 *.jl.mem
 docs/build/
 docs/site/
+*Manifest.toml

.travis.yml

@@ -4,7 +4,9 @@ os:
   - linux
   - osx
 julia:
-  - 1.0
+  - 1.1
+  - 1.2
+
 notifications:
   email: false
 git:
@@ -22,7 +24,7 @@ before_install:
   - if [ "$TRAVIS_OS_NAME" == "linux" ]; then sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E084DAB9; fi
   - if [ "$TRAVIS_OS_NAME" == "linux" ]; then sudo add-apt-repository -y "deb http://cran.rstudio.com/bin/linux/ubuntu $(lsb_release -s -c)/"; fi
   - if [ "$TRAVIS_OS_NAME" == "linux" ]; then sudo apt-get update -qq -y; fi
-  - if [ "$TRAVIS_OS_NAME" == "linux" ]; then sudo apt-get install git r-base r-base-dev r-recommended -y; fi
+  - if [ "$TRAVIS_OS_NAME" == "linux" ]; then sudo apt-get install --allow-unauthenticated git r-base r-base-dev r-recommended -y; fi
 
   # osx
   # faster than using homebrew/science tap
@@ -36,7 +38,7 @@ coveralls: true
 jobs:
   include:
     - stage: "Documentation"
-      julia: 1.0
+      julia: 1.2
       os: linux
       script:
         - julia --project=docs/ -e 'using Pkg; Pkg.instantiate();

Project.toml

@@ -0,0 +1,27 @@
+name = "PhyloPlots"
+uuid = "c0d5b6db-e3fc-52bc-a87d-1d050989ed3b"
+license = "MIT"
+version = "0.2.1"
+
+[deps]
+ColorTypes = "3da002f7-5984-5a60-b8a6-cbb66c0b333f"
+Colors = "5ae59095-9a9b-59fe-a467-6f913c188581"
+DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
+Gadfly = "c91e804a-d5a3-530f-b6f0-dfbca275c004"
+Markdown = "d6f4376e-aef5-505a-96c1-9c027394607a"
+PhyloNetworks = "33ad39ac-ed31-50eb-9b15-43d0656eaa72"
+Printf = "de0858da-6303-5e67-8744-51eddeeeb8d7"
+RCall = "6f49c342-dc21-5d91-9882-a32aef131414"
+
+[compat]
+DataFrames = "≥ 0.13.0"
+Gadfly = "≥ 1.0.0"
+PhyloNetworks = "≥ 0.9.0"
+RCall = "≥ 0.11.0"
+julia = "≥ 0.7.0"
+
+[extras]
+Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
+
+[targets]
+test = ["Test"]

REQUIRE

@@ -7,4 +7,4 @@ DocumenterMarkdown = "997ab1e6-3595-5248-9280-8efb232c3433"
 # PhyloNetworks = "33ad39ac-ed31-50eb-9b15-43d0656eaa72"
 
 [compat]
-Documenter = "~0.21"
+Documenter = "~0.23"

docs/Project.toml

@@ -172,16 +172,16 @@ Check data frame for node annotations:
 """
 function checkNodeDataFrame(net::HybridNetwork, nodeLabel::DataFrame)
     labelnodes = size(nodeLabel,1)>0
-    if (labelnodes && (size(nodeLabel,2)<2 || !(Missings.T(eltype(nodeLabel[1])) <: Integer)))
+    if (labelnodes && (size(nodeLabel,2)<2 || !(Missings.T(eltypes(nodeLabel)[1]) <: Integer)))
         @warn "nodeLabel should have 2+ columns, the first one giving the node numbers (Integer)"
         labelnodes = false
     end
     if labelnodes # remove rows with no node number, check if at least one row remains
-        nodeLabel = nodeLabel[.~ismissing.(nodeLabel[1]),:]
+        filter!(row->!ismissing(row[1]), nodeLabel)
         labelnodes = size(nodeLabel,1)>0
     end
     if labelnodes
-      tmp = setdiff(nodeLabel[1], [n.number for n in net.node])
+      tmp = setdiff(nodeLabel[!,1], [n.number for n in net.node])
       if length(tmp)>0
         msg = "Some node numbers in the nodeLabel data frame are not found in the network:\n"
         for a in tmp msg *= string(" ",a); end
@@ -218,12 +218,12 @@ function prepareNodeDataFrame(net::HybridNetwork, nodeLabel::DataFrame,
         ndf[j,:name] = net.node[i].name
         ndf[j,:num] = string(net.node[i].number)
         if labelnodes
-          jn = findfirst(isequal(net.node[i].number), nodeLabel[1])
+          jn = findfirst(isequal(net.node[i].number), nodeLabel[!,1])
           ndf[j,:lab] = (jn===nothing || ismissing(nodeLabel[jn,2]) ? "" :  # node label not in table or missing
-            (Missings.T(eltype(nodeLabel[2])) <: AbstractFloat ?
+            (Missings.T(eltypes(nodeLabel)[2]) <: AbstractFloat ?
               @sprintf("%0.3g",nodeLabel[jn,2]) : string(nodeLabel[jn,2])))
         end
-        ndf[j,:lea] = net.node[i].leaf # use this later to remove #H? labels
+        ndf[j,:lea] = net.node[i].leaf # use this later to remove H? labels
         ndf[j,:y] = node_y[i]
         ndf[j,:x] = node_x[i]
         j += 1
@@ -256,16 +256,16 @@ function prepareEdgeDataFrame(net::HybridNetwork, edgeLabel::DataFrame, mainTree
                   [Symbol("len"),Symbol("gam"),Symbol("num"),Symbol("lab"),
                    Symbol("hyb"),Symbol("min"),Symbol("x"),Symbol("y")], nrows)
     labeledges = size(edgeLabel,1)>0
-    if (labeledges && (size(edgeLabel,2)<2 || !(Missings.T(eltype(edgeLabel[1])) <: Integer)))
+    if (labeledges && (size(edgeLabel,2)<2 || !(Missings.T(eltypes(edgeLabel)[1]) <: Integer)))
         @warn "edgeLabel should have 2+ columns, the first one giving the edge numbers (Integer)"
         labeledges = false
     end
     if labeledges # remove rows with no edge number and check if at least one remains
-        edgeLabel = edgeLabel[.~ismissing.(edgeLabel[1]),:]
+        filter!(row->!ismissing(row[1]), edgeLabel)
         labeledges = size(edgeLabel,1)>0
     end
     if labeledges
-      tmp = setdiff(edgeLabel[1], [e.number for e in net.edge])
+      tmp = setdiff(edgeLabel[!,1], [e.number for e in net.edge])
       if length(tmp)>0
         msg = "Some edge numbers in the edgeLabel data frame are not found in the network:\n"
         for a in tmp msg *= string(" ",a); end
@@ -280,9 +280,9 @@ function prepareEdgeDataFrame(net::HybridNetwork, edgeLabel::DataFrame, mainTree
             edf[j,:gam] = (net.edge[i].gamma==-1.0  ? "" : @sprintf("%0.3g",net.edge[i].gamma))
             edf[j,:num] = string(net.edge[i].number)
             if labeledges
-              je = findfirst(isequal(net.edge[i].number), edgeLabel[1])
+              je = findfirst(isequal(net.edge[i].number), edgeLabel[!,1])
               edf[j,:lab] = (je===nothing || ismissing(edgeLabel[je,2]) ? "" :  # edge label not found in table
-                (Missings.T(eltype(edgeLabel[2])) <: AbstractFloat ?
+                (Missings.T(eltypes(edgeLabel)[2]) <: AbstractFloat ?
                   @sprintf("%0.3g",edgeLabel[je,2]) : string(edgeLabel[je,2])))
             end
             edf[j,:hyb] = net.edge[i].hybrid

src/phylonetworksPlots.jl

@@ -19,7 +19,7 @@ Plots a network, from left to right.
 - minorHybridEdgeColor: color for minor hybrid edges
 - showEdgeNumber: if true, edges are labelled with the number used internally.
 - showIntNodeLabel: if true, internal nodes are labelled with their names.
-  Useful for hybrid nodes, which do have tags like '#H1'.
+  Useful for hybrid nodes, which do have tags like 'H1'.
 - edgeLabel: dataframe with two columns: the first with edge numbers, the second with labels
   (like bootstrap values) to annotate edges. empty by default.
 - nodeLabel: dataframe with two columns: the first with node numbers, the second with labels
@@ -81,45 +81,45 @@ function Gadfly.plot(net::HybridNetwork; useEdgeLength=false::Bool,
       ndf = prepareNodeDataFrame(net, nodeLabel, showNodeNumber,
               showIntNodeLabel, labelnodes, node_x, node_y)
       if (showTipLabel)
-        push!(mylayers, layer(ndf[ndf[:lea], [:x,:y,:name]], y="y", x="x", label="name",
+        push!(mylayers, layer(ndf[ndf[!,:lea], [:x,:y,:name]], y="y", x="x", label="name",
             Geom.label(position=:right ;hide_overlaps=true))[1])
       end
       if (showIntNodeLabel)
-        push!(mylayers, layer(ndf[.!ndf[:lea], [:x,:y,:name]], y="y", x="x", label="name",
+        push!(mylayers, layer(ndf[.!ndf[!,:lea], [:x,:y,:name]], y="y", x="x", label="name",
             Geom.label(position=:above ;hide_overlaps=true))[1])
       end
       if (showNodeNumber)
         push!(mylayers, layer(ndf, y="y", x="x", label="num",
             Geom.label(position=:dynamic ;hide_overlaps=true))[1])
       end
       if labelnodes
-        push!(mylayers, layer(ndf[[:x,:y,:lab]], y="y", x="x", label="lab",
+        push!(mylayers, layer(ndf[!,[:x,:y,:lab]], y="y", x="x", label="lab",
             Geom.label(position=:left ;hide_overlaps=false))[1])
       end
     end
     # data frame for edge annotations.
     labeledges, edf = prepareEdgeDataFrame(net, edgeLabel, mainTree,
                         edge_xB, edge_xE, edge_yB, edge_yE)
     if labeledges
-      push!(mylayers, layer(edf[[:x,:y,:lab]], y="y", x="x", label="lab",
+      push!(mylayers, layer(edf[!,[:x,:y,:lab]], y="y", x="x", label="lab",
             Geom.label(position=:above ;hide_overlaps=false))[1])
     end
     if (showEdgeLength)
-      push!(mylayers, layer(edf[[:x,:y,:len]], y="y", x="x", label="len",
+      push!(mylayers, layer(edf[!,[:x,:y,:len]], y="y", x="x", label="len",
             Geom.label(position=:below ;hide_overlaps=false))[1])
     end
     if (showGamma && net.numHybrids>0)
       if !mainTree
-        push!(mylayers, layer(edf[edf[:hyb] .& edf[:min], [:x,:y,:gam]], y="y", x="x",label="gam",
+        push!(mylayers, layer(edf[edf[!,:hyb] .& edf[!,:min], [:x,:y,:gam]], y="y", x="x",label="gam",
               Geom.label(position=:below ;hide_overlaps=true),
               Theme(point_label_color=minorHybridEdgeColor))[1])
       end
-      push!(mylayers, layer(edf[edf[:hyb] .& .!edf[:min],[:x,:y,:gam]], y="y", x="x",label="gam",
+      push!(mylayers, layer(edf[edf[!,:hyb] .& .!edf[!,:min], [:x,:y,:gam]], y="y", x="x",label="gam",
             Geom.label(position=:below ;hide_overlaps=true),
             Theme(point_label_color=majorHybridEdgeColor))[1])
     end
     if (showEdgeNumber)
-      push!(mylayers, layer(edf[[:x,:y,:num]], y="y", x="x", label="num",
+      push!(mylayers, layer(edf[!,[:x,:y,:num]], y="y", x="x", label="num",
             Geom.label(position=:dynamic ;hide_overlaps=false))[1])
     end
 

src/plotGadfly.jl

@@ -17,7 +17,7 @@ optional arguments, shared with the Gadfly-based plot function:
 - minorHybridEdgeColor: color for minor hybrid edges
 - showEdgeNumber: if true, edges are labelled with the number used internally.
 - showIntNodeLabel: if true, internal nodes are labelled with their names.
-  Useful for hybrid nodes, which do have tags like '#H1'.
+  Useful for hybrid nodes, which do have tags like 'H1'.
 - edgeLabel: dataframe with two columns: the first with edge numbers, the second with labels
   (like bootstrap values) to annotate edges. empty by default.
 - nodeLabel: dataframe with two columns: the first with node numbers, the second with labels
@@ -81,55 +81,38 @@ function plot(net::HybridNetwork, method::Symbol; useEdgeLength=false::Bool,
     segments($edge_xB, $edge_yB, $edge_xE, $edge_yE, col=$eCol)
     segments($node_x, $node_yB, $node_x, $node_yE, col=$edgeColor)
     """
-    @rput tipcex
     if showTipLabel
-    R"""
-    text($(node_x[leaves])+$tipOffset, $(node_y[leaves]),
-         $(tipLabels(net)), adj=0, font=3, cex=tipcex)
-    """
+      R"text"(node_x[leaves] .+ tipOffset, node_y[leaves],
+              tipLabels(net), adj=0, font=3, cex=tipcex)
     end
     if showIntNodeLabel
-    R"""
-    text($(ndf[.!ndf[:lea],:x]), $(ndf[.!ndf[:lea],:y]),
-         $(ndf[.!ndf[:lea],:name]), adj=c(.5,0))
-    """
+      R"text"(ndf[.!ndf[!,:lea],:x], ndf[.!ndf[!,:lea],:y],
+              ndf[.!ndf[!,:lea],:name], adj=[.5,0])
     end
     if showNodeNumber
-    R"""
-    text($(ndf[:x]), $(ndf[:y]), $(ndf[:num]), adj=1)
-    """
+      R"text"(ndf[!,:x], ndf[!,:y], ndf[!,:num], adj=1)
     end
     if labelnodes
-    R"""
-    text($(ndf[:x]), $(ndf[:y]), $(ndf[:lab]), adj=1)
-    """
+      R"text"(ndf[!,:x], ndf[!,:y], ndf[!,:lab], adj=1)
     end
     labeledges, edf = prepareEdgeDataFrame(net, edgeLabel, mainTree,
                         edge_xB, edge_xE, edge_yB, edge_yE)
     if labeledges
-    R"""
-    text($(edf[:x]), $(edf[:y]), $(edf[:lab]), adj=c(.5,0))
-    """
+      R"text"(edf[!,:x], edf[!,:y], edf[!,:lab], adj=[.5,0])
     end
     if showEdgeLength
-    R"""
-    text($(edf[:x]), $(edf[:y]), $(edf[:len]), adj=c(.5,1))
-    """
+      R"text"(edf[!,:x], edf[!,:y], edf[!,:len], adj=[.5,1.])
     end
     if (showGamma && net.numHybrids>0)
-    im = edf[:hyb] .& edf[:min]
-    iM = edf[:hyb] .& .!edf[:min]
-    R"""
-    text($(edf[im,:x]), $(edf[im,:y]),$(edf[im,:gam]),
-         adj=c(.5,1), col=$minorHybridEdgeColor)
-    text($(edf[iM,:x]), $(edf[iM,:y]),$(edf[iM,:gam]),
-         adj=c(.5,1), col=$majorHybridEdgeColor)
-    """
+      im = edf[!,:hyb] .& edf[!,:min]
+      iM = edf[!,:hyb] .& .!edf[!,:min]
+      R"text"(edf[im,:x], edf[im,:y], edf[im,:gam],
+              adj=[.5,1], col=minorHybridEdgeColor)
+      R"text"(edf[iM,:x], edf[iM,:y], edf[iM,:gam],
+              adj=[.5,1], col=majorHybridEdgeColor)
     end
     if showEdgeNumber
-    R"""
-    text($(edf[:x]), $(edf[:y]), $(edf[:num]), adj=c(.5,0))
-    """
+      R"text"(edf[!,:x], edf[!,:y], edf[!,:num], adj=[.5,0])
     end
     return (xmin, xmax, ymin, ymax, node_x, node_y, node_yB, node_yE,
       edge_xB, edge_xE, edge_yB, edge_yE, ndf, edf)

src/plotRCall.jl

@@ -27,7 +27,7 @@
       1., 5.,1., 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);
-  @test_logs (:warn, "nodeLabel should have 2+ columns, the first one giving the node numbers (Integer)") PhyloPlots.checkNodeDataFrame(net, dat[2:3])
+  @test_logs (:warn, "nodeLabel should have 2+ columns, the first one giving the node numbers (Integer)") PhyloPlots.checkNodeDataFrame(net, dat[!,2:3])
   dat = DataFrame(node=[-5,-3,missing,5],
                   bs=["90","95","99","mytip"],edge=[8,9,4,6]);
   @test PhyloPlots.checkNodeDataFrame(net, dat) == (true,

test/test_phylonetworkPlots.jl

@@ -13,7 +13,7 @@
           majorHybridEdgeColor="tan");
   dat = DataFrame(node=[-5,-10,-1],bs=["90","95","100"],edge=[11,22,26]);
   @test_logs (:warn, "Some node numbers in the nodeLabel data frame are not found in the network:\n -1") plot(net,:RCall, nodeLabel=dat);
-  @test_logs plot(net,:RCall, edgeLabel=dat[[:edge,:bs]]);
+  @test_logs plot(net,:RCall, edgeLabel=dat[!,[:edge,:bs]]);
 
   # plot based on RCall and ape:
   tre = readTopology("(((((((1,2),3),4),5),(6,7)),(8,9)),10);");