-
Notifications
You must be signed in to change notification settings - Fork 13
/
plot.jl
363 lines (324 loc) · 11.1 KB
/
plot.jl
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
# SPDX-License-Identifier: BSD-2-Clause
using RecipesBase
@recipe function f(tree::Phylo.AbstractTree; treetype = :dendrogram,
marker_group = nothing, line_group = nothing,
showtips = true, tipfont = (7,))
linecolor --> :black
grid --> false
framestyle --> :none
legend --> false
colorbar --> true
size --> (1000, 1000)
d, h, n = _findxy(tree)
adj = 0.03maximum(values(d))
tipannotations = map(x -> (d[x] + adj, h[x], x), getleafnames(tree))
lz = get(plotattributes, :line_z, nothing)
mz = get(plotattributes, :marker_z, nothing)
isnothing(lz) || (line_z := _handlez(lz, tree, n))
isnothing(mz) || (marker_z := _handlez(mz, tree, n))
mg = _handlez(marker_group, tree, n)
lg = _handlez(line_group, tree, n)
x, y = Float64[], Float64[]
for node in n
if hasinbound(tree, node)
push!(x, d[getparent(tree, node)], d[getparent(tree, node)],
d[node], NaN)
push!(y, h[getparent(tree, node)], h[node], h[node], NaN)
end
end
marker_x, marker_y = _handlemarkers(plotattributes, mg, tree, d, h, n)
if treetype == :dendrogram
Dendrogram(x, y, tipannotations, marker_x, marker_y, showtips, tipfont,
mg, lg)
elseif treetype == :fan
Fan(x, y, tipannotations, marker_x, marker_y, showtips, tipfont, mg, lg)
else
throw(ArgumentError("Unsupported `treetype`; valid values are `:dendrogram` or `:fan`"))
end
end
struct Dendrogram
x::Any
y::Any
tipannotations::Any
marker_x::Any
marker_y::Any
showtips::Any
tipfont::Any
marker_group::Any
line_group::Any
end
struct Fan
x::Any
y::Any
tipannotations::Any
marker_x::Any
marker_y::Any
showtips::Any
tipfont::Any
marker_group::Any
line_group::Any
end
@recipe function f(dend::Dendrogram)
ex = extrema(filter(isfinite, dend.x))
xlims --> (ex[1] - 0.05 * ex[2], ex[2] * 1.15)
# tip annotations
dend.showtips &&
(annotations := map(x -> (x[1], x[2], (x[3], :left, dend.tipfont...)),
dend.tipannotations))
sa = get(plotattributes, :series_annotations, nothing)
@series begin
seriestype := :path
markersize := 0
markershape := :none
series_annotations := nothing
label --> ""
# primary := false
lc = _extend(get(plotattributes, :linecolor, nothing), dend.x)
lc !== nothing && (linecolor := lc)
la = _extend(get(plotattributes, :linealpha, nothing), dend.x)
la !== nothing && (linealpha := la)
lz = _extend(get(plotattributes, :line_z, nothing), dend.x)
lz !== nothing && (line_z := lz)
dend.x, dend.y
end
if !isempty(dend.marker_x) || sa !== nothing
if isnothing(dend.marker_group)
@series begin
seriestype := :scatter
sa !== nothing && (series_annotations := sa)
label --> ""
dend.marker_x, dend.marker_y
end
else
groups = sort(unique(dend.marker_group))
for group in groups
idxs = findall(==(group), dend.marker_group)
@series begin
seriestype := :scatter
sa !== nothing && (series_annotations := sa[idxs])
label --> string(group)
dend.marker_x[idxs], dend.marker_y[idxs]
end
end
end
end
primary := false
label := ""
return nothing
end
@recipe function f(fan::Fan)
adjust(y) = 2pi * y / (length(fan.tipannotations) + 1)
aspect_ratio := 1
# tip annotations
mx = maximum(filter(isfinite, fan.x))
if fan.showtips
xlims --> (1.5 .* (-mx, mx))
ylims --> (1.5 .* (-mx, mx))
annotations := map(x -> (_tocirc(x[1], adjust(x[2]))...,
(x[3], :left,
rad2deg(adjust(x[2])), fan.tipfont...)),
fan.tipannotations)
end
sa = get(plotattributes, :series_annotations, nothing)
@series begin
seriestype := :path
markersize := 0
markershape := :none
series_annotations := nothing
label := ""
x, y = _circle_transform_segments(fan.x, adjust(fan.y))
lc = _extend(get(plotattributes, :linecolor, nothing), x)
lc !== nothing && (linecolor := lc)
la = _extend(get(plotattributes, :linealpha, nothing), x)
la !== nothing && (linealpha := la)
lz = _extend(get(plotattributes, :line_z, nothing), x)
lz !== nothing && (line_z := lz)
x, y
end
if !isempty(fan.marker_x) || sa !== nothing
if isnothing(fan.marker_group)
@series begin
seriestype := :scatter
sa !== nothing && (series_annotations := sa)
label --> ""
_xcirc.(adjust(fan.marker_y), fan.marker_x),
_ycirc.(adjust(fan.marker_y), fan.marker_x)
end
else
groups = sort(unique(fan.marker_group))
for group in groups
idxs = findall(==(group), fan.marker_group)
@series begin
seriestype := :scatter
sa !== nothing && (series_annotations := sa[idxs])
label --> string(group)
_xcirc.(adjust(fan.marker_y[idxs]), fan.marker_x[idxs]),
_ycirc.(adjust(fan.marker_y[idxs]), fan.marker_x[idxs])
end
end
end
end
primary := false
label := ""
return nothing
end
_handlez(x, tree, names) = x
function _handlez(x::Union{String, Symbol}, tree, names)
return [getnodedata(tree, name, x) for name in names]
end
function _handlez(x::Dict, tree, names)
ret = fill(NaN, length(names))
for (i, n) in enumerate(names)
name = getnodename(tree, n)
if haskey(x, name)
ret[i] = x[name]
end
end
return ret
end
_mylength(x) = 1
_mylength(x::AbstractVector) = length(x)
function _handlemarkers(plotattributes, marker_group, tree, d, h, names)
isnothing(marker_group) || (plotattributes[:marker_group] = marker_group)
markerfields = filter(x -> occursin(r"marker", String(x)),
keys(plotattributes))
isempty(markerfields) && return (Float64[], Float64[])
maxlength = maximum([_mylength(plotattributes[k]) for k in markerfields])
if maxlength ∈ (1, ninternal(tree))
names = filter(node -> !isleaf(tree, node), names)
end
return [d[node] for node in names], [h[node] for node in names]
end
function _extend(tmp, x)
tmp isa AbstractVector && abs(length(tmp) - count(isnan, x)) < 2 ||
return nothing
ret = similar(x, eltype(tmp))
j = 1 + length(tmp) - count(isnan, x)
for i in eachindex(x)
ret[i] = tmp[j]
isnan(x[i]) && (j += 1)
end
return ret
end
"""
sort!(::AbstractTree; rev = false)
Sorts the branches descending from each node by total number of
descendants. This creates a clearer tree for plotting. The
process is also called "ladderizing" the tree. Use `rev=true` to
reverse the sorting order.
"""
function Base.sort!(tree::T; rev = false) where {T <: AbstractTree}
function loc!(clade::String)
if isleaf(tree, clade)
return 1
end
sizes = map(loc!, getchildren(tree, clade))
node = getnode(tree, clade)
if T <: LinkTree
node.other .= node.other[sortperm(sizes, rev = rev)]
elseif T <: RecursiveTree
node.conns .= node.conns[sortperm(sizes, rev = rev)]
end
return sum(sizes) + 1
end
loc!(first(nodenamefilter(isroot, tree)))
return tree
end
"""
sort(::AbstractTree; rev = false)
Copies a tree and sorts its branches. See `sort!` for further details.
"""
Base.sort(tree::AbstractTree; rev = false) = sort!(copy(tree))
function _nodedepths(tree::Phylo.AbstractTree)
function finddepths!(clade::String)
if !in(clade, keys(depth))
for subclade in getchildren(tree, clade)
finddepths!(subclade)
end
end
if !isleaf(tree, clade)
ch_depths = [depth[child] for child in getchildren(tree, clade)]
depth[clade] = (maximum(ch_depths) + minimum(ch_depths)) / 2.0
end
end
depth = Dict(tip => float(i)
for (i, tip) in enumerate(getnodename(tree, x)
for x in traversal(tree, preorder)
if isleaf(tree, x)))
sizehint!(depth, nnodes(tree))
root = getnodename(tree, getroot(tree))
finddepths!(root)
return depth
end
function _findxy(tree::Phylo.AbstractTree)
height = nodeheights(tree)
depth = _nodedepths(tree)
return height, depth, AxisArrays.axes(height, 1).val
end
function _find_tips(height, depth, tree)
x, y, l = Float64[], Float64[], String[]
for k in keys(height)
if isleaf(tree, k)
push!(x, height[k])
push!(y, depth[k])
push!(l, k)
end
end
return x, y, l
end
function _p_circ(start_θ, end_θ, r = 1)
steps = range(start_θ, stop = end_θ,
length = 1 + ceil(Int, 60abs(end_θ - start_θ)))
retx = Array{Float64}(undef, length(steps))
rety = similar(retx)
for u in eachindex(steps)
retx[u] = _xcirc(steps[u], r)
rety[u] = _ycirc(steps[u], r)
end
return retx, rety
end
_xcirc(x, r) = r * cos(x)
_ycirc(y, r) = r * sin(y)
_tocirc(x, y) = _xcirc(y, x), _ycirc(y, x)
function _circle_transform_segments(xs, ys)
retx, rety = Float64[], Float64[]
function _transform_seg(_x, _y)
tmpx, tmpy = _p_circ(_y[1], _y[2], _x[1])
append!(retx, tmpx)
append!(rety, tmpy)
push!(retx, _xcirc(_y[3], _x[3]), NaN)
return push!(rety, _ycirc(_y[3], _x[3]), NaN)
end
i = 1
while !isnothing(i) && i < length(xs)
j = findnext(isnan, xs, i) - 1
_transform_seg(view(xs, i:j), view(ys, i:j))
i = j + 2
end
return retx, rety
end
"""
map_depthfirst(FUN, start, tree, eltype = nothing)
Apply `FUN` to each node in `tree` in depth-first order, and return the result.
`FUN` must take two arguments, `val` and `node`, where `val` is the result of
applying `FUN` to the previous node, and `node` is the current node. `start`
specifies the initial value of `val`, and `eltype` specifies the type of the
return value of `FUN`.
### Examples
≡≡≡≡≡≡≡≡≡≡≡
Define a function to evolve a trait on the tree according to Brownian motion
julia> evolve(tree) = map_depthfirst((val, node) -> val + randn(), 0., tree, Float64)
"""
function map_depthfirst(FUN, start, tree, eltype = nothing)
root = first(nodenamefilter(isroot, tree))
isnothing(eltype) && (eltype = typeof(FUN(start, root)))
ret = Vector{eltype}()
function local!(val, node)
push!(ret, val)
for ch in getchildren(tree, node)
local!(FUN(val, node), ch)
end
end
local!(start, root)
return ret
end