From cc6683254a091d9028e8065be451af42d3f2c305 Mon Sep 17 00:00:00 2001 From: Jorge Fernandez-de-Cossio-Diaz Date: Sun, 22 Jan 2023 02:38:39 +0100 Subject: [PATCH] makie --- Artifacts.toml | 7 + Project.toml | 6 +- docs/Artifacts.toml | 7 + docs/Project.toml | 11 +- docs/src/literate/rfam.jl | 41 +- src/SequenceLogos.jl | 18 +- src/makie.jl | 99 +-- test/Manifest.toml | 1282 ++++++++++++++++++++++++++++++++++++- test/Project.toml | 6 +- test/runtests.jl | 28 +- 10 files changed, 1415 insertions(+), 90 deletions(-) create mode 100644 Artifacts.toml create mode 100644 docs/Artifacts.toml diff --git a/Artifacts.toml b/Artifacts.toml new file mode 100644 index 0000000..3f6631c --- /dev/null +++ b/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" diff --git a/Project.toml b/Project.toml index 355f18e..ed3d9f3 100644 --- a/Project.toml +++ b/Project.toml @@ -4,10 +4,8 @@ authors = "Jorge Fernandez-de-Cossio-Diaz " 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" diff --git a/docs/Artifacts.toml b/docs/Artifacts.toml new file mode 100644 index 0000000..3f6631c --- /dev/null +++ b/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" diff --git a/docs/Project.toml b/docs/Project.toml index 3343bf6..38447d2 100644 --- a/docs/Project.toml +++ b/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" diff --git a/docs/src/literate/rfam.jl b/docs/src/literate/rfam.jl index e872159..22d7160 100644 --- a/docs/src/literate/rfam.jl +++ b/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, '-' => '⊟')) diff --git a/src/SequenceLogos.jl b/src/SequenceLogos.jl index baf9b68..a875e83 100644 --- a/src/SequenceLogos.jl +++ b/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 diff --git a/src/makie.jl b/src/makie.jl index bbad7b9..485b0dc 100644 --- a/src/makie.jl +++ b/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 diff --git a/test/Manifest.toml b/test/Manifest.toml index 6024ab2..b54defb 100644 --- a/test/Manifest.toml +++ b/test/Manifest.toml @@ -1,39 +1,1289 @@ # This file is machine-generated - editing it directly is not advised -[[Base64]] +julia_version = "1.8.4" +manifest_format = "2.0" +project_hash = "7eba06fcaddbce789e7db5c4e1bc1d0d64b003fa" + +[[deps.AbstractFFTs]] +deps = ["ChainRulesCore", "LinearAlgebra"] +git-tree-sha1 = "69f7020bd72f069c219b5e8c236c1fa90d2cb409" +uuid = "621f4979-c628-5d54-868e-fcf4e3e8185c" +version = "1.2.1" + +[[deps.AbstractTrees]] +git-tree-sha1 = "faa260e4cb5aba097a73fab382dd4b5819d8ec8c" +uuid = "1520ce14-60c1-5f80-bbc7-55ef81b5835c" +version = "0.4.4" + +[[deps.Adapt]] +deps = ["LinearAlgebra"] +git-tree-sha1 = "0310e08cb19f5da31d08341c6120c047598f5b9c" +uuid = "79e6a3ab-5dfb-504d-930d-738a2a938a0e" +version = "3.5.0" + +[[deps.Animations]] +deps = ["Colors"] +git-tree-sha1 = "e81c509d2c8e49592413bfb0bb3b08150056c79d" +uuid = "27a7e980-b3e6-11e9-2bcd-0b925532e340" +version = "0.4.1" + +[[deps.ArgTools]] +uuid = "0dad84c5-d112-42e6-8d28-ef12dabb789f" +version = "1.1.1" + +[[deps.Artifacts]] +uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33" + +[[deps.Automa]] +deps = ["Printf", "ScanByte", "TranscodingStreams"] +git-tree-sha1 = "d50976f217489ce799e366d9561d56a98a30d7fe" +uuid = "67c07d97-cdcb-5c2c-af73-a7f9c32a568b" +version = "0.8.2" + +[[deps.AxisAlgorithms]] +deps = ["LinearAlgebra", "Random", "SparseArrays", "WoodburyMatrices"] +git-tree-sha1 = "66771c8d21c8ff5e3a93379480a2307ac36863f7" +uuid = "13072b0f-2c55-5437-9ae7-d433b7a33950" +version = "1.0.1" + +[[deps.AxisArrays]] +deps = ["Dates", "IntervalSets", "IterTools", "RangeArrays"] +git-tree-sha1 = "1dd4d9f5beebac0c03446918741b1a03dc5e5788" +uuid = "39de3d68-74b9-583c-8d2d-e117c070f3a9" +version = "0.4.6" + +[[deps.Base64]] uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f" -[[Distributed]] +[[deps.BioGenerics]] +deps = ["TranscodingStreams"] +git-tree-sha1 = "0b581906418b93231d391b5dd78831fdc2da0c82" +uuid = "47718e42-2ac5-11e9-14af-e5595289c2ea" +version = "0.1.2" + +[[deps.BioSequences]] +deps = ["BioSymbols", "Random", "SnoopPrecompile", "Twiddle"] +git-tree-sha1 = "e67b5446b44d96595ededa2b32ab0f2f6b3d2997" +uuid = "7e6ae17a-c86d-528c-b3b9-7f778a29fe59" +version = "3.1.2" + +[[deps.BioSymbols]] +deps = ["SnoopPrecompile"] +git-tree-sha1 = "2052c3ec7c41b69efa0e9ff7e2734aa6658d4c40" +uuid = 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+version = "3.5.0+0" diff --git a/test/Project.toml b/test/Project.toml index 4e8527a..b1d0009 100644 --- a/test/Project.toml +++ b/test/Project.toml @@ -1,3 +1,7 @@ [deps] -SafeTestsets = "1bc83da4-3b8d-516f-aca4-4fe02f6d838f" +CairoMakie = "13f3f980-e62b-5c42-98c6-ff1f3baf88f0" +FASTX = "c2308a5c-f048-11e8-3e8a-31650f418d12" +LogExpFunctions = "2ab3a3ac-af41-5b50-aa03-7779005ae688" +Makie = "ee78f7c6-11fb-53f2-987a-cfe4a2b5a57a" +Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2" Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40" diff --git a/test/runtests.jl b/test/runtests.jl index 593f765..0878488 100644 --- a/test/runtests.jl +++ b/test/runtests.jl @@ -1 +1,27 @@ -using SafeTestsets +using Test: @test +using SequenceLogos: __example_fasta, makie_sequence_logo! +using Statistics: mean +using LogExpFunctions: xlogx +import FASTX +using Base: front +import Makie, CairoMakie + +records = collect(FASTX.FASTA.Reader(open(__example_fasta()))) +seqs = FASTX.sequence.(records) + +NTs = "ACGU-" + +function onehot(s::AbstractString) + return reshape(collect(s), 1, length(s)) .== collect(NTs) +end +X = reshape(reduce(hcat, onehot.(seqs)), length(NTs), :, length(seqs)) + +p = reshape(mean(X; dims=3), size(X, 1), size(X, 2)) +H = sum(-xlogx.(p) / log(2); dims=1) +cons = p .* (log2(5) .- H) + + +fig = Makie.Figure() +ax = Makie.Axis(fig[1,1]; width=500, height=200) +makie_sequence_logo!(ax, cons, collect(NTs), [:red, :blue, :orange, :green, :black]) +fig