Merge pull request #31 from MurrellGroup/Phylo-svg-tree-export

Respond to #24

Project.toml

@@ -7,7 +7,6 @@ version = "0.1.0"
 AbstractMCMC = "80f14c24-f653-4e6a-9b94-39d6b0f70001"
 AdvancedHMC = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d"
 CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"
-Compose = "a81c6b42-2e10-5240-aca2-a61377ecd94b"
 DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
 Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
 FASTX = "c2308a5c-f048-11e8-3e8a-31650f418d12"
@@ -21,6 +20,7 @@ MolecularEvolution = "9f975960-e239-4209-8aa0-3d3ad5a82892"
 NLopt = "76087f3c-5699-56af-9a33-bf431cd00edd"
 NNlib = "872c559c-99b0-510c-b3b7-b6c96a88d5cd"
 ParameterHandling = "2412ca09-6db7-441c-8e3a-88d5709968c5"
+Phylo = "aea672f4-3940-5932-aa44-993d1c3ff149"
 Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
 SimpleUnPack = "ce78b400-467f-4804-87d8-8f486da07d0a"
 StatsBase = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91"

src/CodonMolecularEvolution.jl

@@ -1,6 +1,6 @@
 module CodonMolecularEvolution
 
-using FASTX, MolecularEvolution, Measures, Compose, Plots, StatsBase, Distributions, DataFrames, CSV, NLopt, ParameterHandling, LinearAlgebra
+using FASTX, MolecularEvolution, Measures, Plots, StatsBase, Distributions, DataFrames, CSV, NLopt, ParameterHandling, LinearAlgebra, Phylo
 using NNlib, Distributions, Zygote, AdvancedHMC, LogDensityProblems, SimpleUnPack, AbstractMCMC, LogDensityProblemsAD, Interpolations, MCMCChains
 
 abstract type difFUBARGrid end

src/difFUBAR/difFUBAR.jl

@@ -180,14 +180,17 @@ function difFUBAR_init(outpath_and_file_prefix, treestring, tags; tag_colors=DIF
     push!(tag_colors, "black") #ASSUMPTION: background color is always black
 
     if exports
-        #Replace with Phylo.jl based plot?
-        color_dict = Dict(zip(getnodelist(tree), [tag_colors[model_ind(n.name, tags)] for n in getnodelist(tree)]))
-        label_dict = Dict(zip(getnodelist(tree), [strip_tags_from_name(n.name) for n in getnodelist(tree)]))
-        img = tree_draw(tree, canvas_height=(3 + length(getleaflist(tree)) / 5)cm,
-            draw_labels=true, dot_color_dict=color_dict,
-            line_color_dict=color_dict, line_width=0.3, min_dot_size=0.01,
-            nodelabel_dict=label_dict)
-        img |> SVG(analysis_name * "_tagged_input_tree.svg", 15cm, (3 + length(getleaflist(tree)) / 5)cm)
+        #TODO: update plots in docs
+        phylo_tree = get_phylo_tree(tree)
+        tagging = [tag_colors[model_ind(n, tags)] for n in nodenameiter(phylo_tree)]
+        for node in nodeiter(phylo_tree)
+            renamenode!(phylo_tree, node, strip_tags_from_name(node.name))
+        end
+        #Warnings regarding marker- and linecolor also appear in the Phylo.jl docs example
+        #Note: sometimes long leafnames are truncated/not visible in the plot
+        pl = plot(phylo_tree,
+            showtips = true, tipfont = 6, markercolor = tagging, linecolor = tagging, markerstrokewidth = 0, size = (600, (120 + length(getleaflist(tree)) * 8)))
+        savefig_tweakSVG(analysis_name * "_tagged_input_tree.svg", pl)
     end
 
     #Tags and tag colors are now ordered, and tag_colors includes the untagged category

src/difFUBAR/grids.jl

@@ -232,7 +232,7 @@ function gridprep(tree, tags; verbosity = 1, foreground_grid = 6, background_gri
     length(background_omega_grid) * length(alphagrid) * length(omegagrid)^2
 
     num_groups = length(tags)
-    is_background = maximum([model_ind(n.name, tags) for n in getnodelist(tree) if !isroot(n)]) > num_groups
+    is_background = maximum([model_ind(n.name, tags) for n in getnodelist(tree) if !MolecularEvolution.isroot(n)]) > num_groups
     tensor_dims = 1+num_groups+is_background;
 
     codon_param_vec = [[a] for a in alphagrid]