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Respond to #24 #31

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2 changes: 1 addition & 1 deletion Project.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,6 @@ version = "0.1.0"

[deps]
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"
Expand All @@ -14,6 +13,7 @@ Measures = "442fdcdd-2543-5da2-b0f3-8c86c306513e"
MolecularEvolution = "9f975960-e239-4209-8aa0-3d3ad5a82892"
NLopt = "76087f3c-5699-56af-9a33-bf431cd00edd"
ParameterHandling = "2412ca09-6db7-441c-8e3a-88d5709968c5"
Phylo = "aea672f4-3940-5932-aa44-993d1c3ff149"
Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
StatsBase = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91"

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2 changes: 1 addition & 1 deletion src/CodonMolecularEvolution.jl
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@@ -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

abstract type difFUBARGrid end

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19 changes: 11 additions & 8 deletions src/difFUBAR/difFUBAR.jl
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Expand Up @@ -173,14 +173,17 @@ 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
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