makie

Artifacts.toml

@@ -0,0 +1,7 @@
+[RF00162_trimmed]
+git-tree-sha1 = "de354c34ade084ac3634c94c2ea4ede8ed721ea8"
+lazy = true
+
+    [[RF00162_trimmed.download]]
+    sha256 = "c90ab58f8c2b290dc44f9aac6ea2c5d03d476acf7f96fd938d68bbf36c20d9bf"
+    url = "https://gist.github.com/cossio/16360fcfdbddbd13430d485f0000e379/raw/de354c34ade084ac3634c94c2ea4ede8ed721ea8.tar.gz"

Project.toml

@@ -4,10 +4,8 @@ authors = "Jorge Fernandez-de-Cossio-Diaz <[email protected]>"
 version = "0.2.2-DEV"
 
 [deps]
-PyPlot = "d330b81b-6aea-500a-939a-2ce795aea3ee"
-Colors = "5ae59095-9a9b-59fe-a467-6f913c188581"
+LazyArtifacts = "4af54fe1-eca0-43a8-85a7-787d91b784e3"
+Makie = "ee78f7c6-11fb-53f2-987a-cfe4a2b5a57a"
 
 [compat]
 julia = "1.6"
-PyPlot = "2.9"
-Colors = "0.12"

docs/Artifacts.toml

@@ -0,0 +1,7 @@
+[RF00162_trimmed]
+git-tree-sha1 = "de354c34ade084ac3634c94c2ea4ede8ed721ea8"
+lazy = true
+
+    [[RF00162_trimmed.download]]
+    sha256 = "c90ab58f8c2b290dc44f9aac6ea2c5d03d476acf7f96fd938d68bbf36c20d9bf"
+    url = "https://gist.github.com/cossio/16360fcfdbddbd13430d485f0000e379/raw/de354c34ade084ac3634c94c2ea4ede8ed721ea8.tar.gz"

docs/Project.toml

@@ -1,15 +1,10 @@
 [deps]
-AlgebraOfGraphics = "cbdf2221-f076-402e-a563-3d30da359d67"
+CairoMakie = "13f3f980-e62b-5c42-98c6-ff1f3baf88f0"
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
 Downloads = "f43a241f-c20a-4ad4-852c-f6b1247861c6"
-GitHub = "bc5e4493-9b4d-5f90-b8aa-2b2bcaad7a26"
-Gzip_jll = "be1be57a-8558-53c3-a7e5-50095f79957e"
-LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
+LazyArtifacts = "4af54fe1-eca0-43a8-85a7-787d91b784e3"
 Literate = "98b081ad-f1c9-55d3-8b20-4c87d4299306"
 LogExpFunctions = "2ab3a3ac-af41-5b50-aa03-7779005ae688"
-MLDatasets = "eb30cadb-4394-5ae3-aed4-317e484a6458"
 Makie = "ee78f7c6-11fb-53f2-987a-cfe4a2b5a57a"
-PyPlot = "d330b81b-6aea-500a-939a-2ce795aea3ee"
-Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
-Rfam = "38c5b72b-a3f0-437e-9f79-f3da4655de63"
+SequenceLogos = "7a3f67ce-6eeb-4904-9da4-2cbd106a5944"
 Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"

docs/src/literate/rfam.jl

@@ -2,24 +2,23 @@
 # SequenceLogos examples with RFAM
 =#
 
-import GitHub
-import PyPlot
 import SequenceLogos
-using Downloads: download
+using LazyArtifacts: LazyArtifacts, @artifact_str
+import Makie
+import CairoMakie
 using Statistics: mean
 using LogExpFunctions: xlogx
 
-# Fetch RNA family alignment RF00162 from RFAM (pre-stored as a Github Gist)
 
-data = GitHub.gist("b63e87024fac287a1800b1555276a04b")
-url = data.files["RF00162-trimmed.afa"]["raw_url"]
-path = download(url; timeout = Inf)
+import PyPlot
+
+# Fetch RNA family alignment RF00162 from RFAM (pre-stored as a Github Gist)
+fasta_path = joinpath(artifact"RF00162_trimmed", "RF00162-trimmed.afa")
 nothing #hide
 
 # Parse lines
-
 seqs = String[]
-for line in eachline(path)
+for line in eachline(fasta_path)
     if startswith(line, '>')
         continue
     else
@@ -37,10 +36,30 @@ function onehot(s::String)
     return reshape(collect(s), 1, length(s)) .== collect(NTs)
 end
 X = reshape(reduce(hcat, onehot.(seqs)), 5, :, length(seqs));
+p = reshape(mean(X; dims=3), size(X)[1:2]...)
+xlog2x(x) = xlogx(x) / log(oftype(x,2))
+H = sum(-xlog2x.(p); dims=1)
+
+weights = cons = p .* (log2(5) .- H)
+
+letters = collect(NTs)
+colors = [:red, :red, :blue, :blue, :black]
+
+fig = Makie.Figure()
+ax = Makie.Axis(fig[1,1], width=600, height=100)
+SequenceLogos.makie_sequence_logo!(ax, cons, letters, colors)
+Makie.resize_to_layout!(fig)
+fig
+
+function plot_example()
+    fig = Makie.Figure()
+    ax = Makie.Axis(fig[1,1], width=600, height=100)
+    SequenceLogos.makie_sequence_logo!(ax, cons, letters, colors)
+    Makie.resize_to_layout!(fig)
+    fig
+end
 
-# Sequence logo
 
-xlog2x(x) = xlogx(x) / log(oftype(x,2))
 logo_from_matrix(w::AbstractMatrix) = SequenceLogos.logo_from_matrix(w, replace(NTs, '-' => '⊟'))
 
 

src/SequenceLogos.jl

@@ -1,8 +1,18 @@
 module SequenceLogos
 
-include("logo.jl")
-include("color_funs.jl")
-include("pyplot.jl")
-include("bio.jl")
+import Makie
+
+using LazyArtifacts: LazyArtifacts, @artifact_str
+import Makie
+
+#include("logo.jl")
+#include("color_funs.jl")
+#include("pyplot.jl")
+#include("bio.jl")
+include("makie.jl")
+
+function __example_fasta()
+    return joinpath(artifact"RF00162_trimmed", "RF00162-trimmed.afa")
+end
 
 end # module

src/makie.jl

@@ -1,64 +1,73 @@
-import CairoMakie
-import Makie
-
-struct SeqLogo{W<:AbstractMatrix,L<:AbstractVecOrMat,C<:AbstractVecOrMat}
-    weights::W
-    letters::L
-    colors::C
-    function SeqLogo{W,L,C}(weights::W, letters::L, colors::C) where {W<:AbstractMatrix,L<:AbstractVector,C<:AbstractVector}
-        @assert size(weights, 1) == length(letters) == length(colors)
-        return new{W,L,C}(weights, letters, colors)
-    end
-    function SeqLogo{W,L,C}(weights::W, letters::L, colors::C) where {W<:AbstractMatrix,L<:AbstractMatrix,C<:AbstractMatrix}
-        @assert size(weights) == size(letters) == size(colors)
-        return new{W,L,C}(weights, letters, colors)
-    end
-end
-
-function SeqLogo(weights::W, letters::L, colors::C) where {W,L,C}
-    return SeqLogo{W,L,C}(weights, letters, colors)
-end
-
-function sort_logo(logo::SeqLogo)
-    weights = similar(logo.weights)
-    letters = similar(logo.letters, size(weights))
-    colors = similar(logo.colors, size(weights))
-    for i in axes(weights, 1)
-        p = sortperm(logo.weights[i,:])
-        weights[i, :] .= logo.weights[i, p]
-        letters[i, :] .= logo.letters[p]
-        colors[i, :] .= logo.colors[p]
-    end
-    return SeqLogo(weights, letters, colors)
-end
-
 function makie_sequence_logo!(
     ax::Makie.Axis, weights::AbstractMatrix, letters::AbstractMatrix, colors::AbstractMatrix
 )
     @assert size(weights) == size(letters) == size(colors)
 
+    # for i in axes(weights, 2)
+    #     y_pos = y_neg = 0.0
+    #     for k in axes(weights, 1)
+    #         if weights[k,i] > 0
+    #             y = y_pos
+    #             y_pos += weights[k,i]
+    #         elseif weights[k,i] < 0
+    #             y = y_neg
+    #             y_neg += weights[k,i]
+    #         end
+
+    #         Makie.text!(
+    #             ax, i, y; text=string(letters[k,i]),
+    #             textsize=abs(weights[k,i]), scale=Makie.Vec2(1/abs(weights[k,i]), 1),
+    #             color=colors[k,i],
+    #             markerspace=:data, align=(:center, :baseline), font="Arial bold"
+    #         )
+    #         Makie.scale
+    #     end
+    # end
+
+
+   # return nothing
+
     x = repeat((1:size(weights, 2))', size(weights, 1), 1)
     y = zero(weights)
-    for i in axes(weights, 1)
+    for i in axes(weights, 2)
         y_pos = y_neg = 0.0
-        for j in axes(weights, 2)
-            if weights[i,j] > 0
-                y_pos += weights[i,j]
-                y[i,j] = y_pos
-            elseif weights[i,j] < 0
-                y_neg += weights[i,j]
-                y[i,j] = y_neg
+        for k in axes(weights, 1)
+            if weights[k,i] > 0
+                y[k,i] = y_pos + weights[k,i]/2
+                y_pos += weights[k,i]
+            elseif weights[k,i] < 0
+                y[k,i] = y_neg + weights[k,i]/2
+                y_neg += weights[k,i]
             end
         end
     end
 
-    Makie.text!(ax, vec(x), vec(y); text=vec(letters), textsize=vec(abs.(weights)))
+    Makie.text!(
+        ax, vec(x), vec(y); text=vec(letters),
+        fontsize=vec([Makie.Vec2(1, abs(w)) for w in weights]),
+        color=vec(colors),
+        markerspace=:data, align=(:center, :baseline), font="Arial"
+    )
 end
 
 function makie_sequence_logo!(
     ax::Makie.Axis, weights::AbstractMatrix, letters::AbstractVector, colors::AbstractVector
 )
     @assert size(weights, 1) == length(letters) == length(colors)
-    weights_sorted, letters_sorted, colors_sorted = sort_sequence_logo(weights, letters, colors)
-    return makie_seqlogo!(ax, weights_sorted, letters_sorted, colors_sorted)
+    sorted_weights, sorted_letters, sorted_colors = sort_logo(weights, letters, colors)
+    return makie_sequence_logo!(ax, sorted_weights, sorted_letters, sorted_colors)
+end
+
+function sort_logo(weights::AbstractMatrix, letters::AbstractVector, colors::AbstractVector)
+    @assert size(weights, 1) == length(letters) == length(colors)
+    sorted_weights = similar(weights)
+    sorted_letters = similar(letters, size(weights))
+    sorted_colors = similar(colors, size(weights))
+    for i in axes(weights, 2)
+        p = sortperm(weights[:,i])
+        sorted_weights[:,i] .= weights[p,i]
+        sorted_letters[:,i] .= letters[p]
+        sorted_colors[:,i] .= colors[p]
+    end
+    return sorted_weights, sorted_letters, sorted_colors
 end