From 5d75f3394071ecaefe6004070b94ea4f11a6ca30 Mon Sep 17 00:00:00 2001 From: minsoo Date: Sun, 2 Oct 2022 10:51:07 -0700 Subject: [PATCH] v0.1.5 --- Project.toml | 2 +- docs/make.jl | 2 +- docs/src/examples/{chip.md => peaks.md} | 11 ++--------- src/plotloops.jl | 1 + 4 files changed, 5 insertions(+), 11 deletions(-) rename docs/src/examples/{chip.md => peaks.md} (93%) diff --git a/Project.toml b/Project.toml index 56b50cd..b3279da 100644 --- a/Project.toml +++ b/Project.toml @@ -1,7 +1,7 @@ name = "GeneticsMakie" uuid = "8ca62643-82d8-47b5-a233-a06d1654fb35" authors = ["Minsoo and contributors"] -version = "0.1.4" +version = "0.1.5" [deps] CairoMakie = "13f3f980-e62b-5c42-98c6-ff1f3baf88f0" diff --git a/docs/make.jl b/docs/make.jl index f5adaee..f940a15 100644 --- a/docs/make.jl +++ b/docs/make.jl @@ -25,7 +25,7 @@ makedocs(; "Plotting GWAS" => "examples/gwas.md", "Plotting TWAS" => "examples/twas.md", "Plotting loops" => "examples/loops.md", - "Plotting peaks" => "examples/chip.md"], + "Plotting peaks" => "examples/peaks.md"], "API" => "api.md", ], ) diff --git a/docs/src/examples/chip.md b/docs/src/examples/peaks.md similarity index 93% rename from docs/src/examples/chip.md rename to docs/src/examples/peaks.md index c2d5754..3192965 100644 --- a/docs/src/examples/chip.md +++ b/docs/src/examples/peaks.md @@ -1,15 +1,8 @@ -# Plotting ChIP-seq and ATAC-seq +# Plotting peaks Epigenetic sequencing is another data modality of interest that we can visualize with [__Makie.jl__](https://makie.juliaplots.org/stable/) and -GeneticsMakie.jl. Chromatin immunoprecipitation sequencing (ChIP-seq) and assay -for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) -map epigenetic modifications throughout the genome by identifying DNA-protein -interaction sites and open chromatin respectively, and although they capture -different aspects of the epigenome, their resulting data share the same form -and function (BAM files to capture reads, wiggle files to capture coverage and -signal, BED files to capture peaks). Consequently, visualizing both types of -sequencing will follow the same workflow. +GeneticsMakie.jl. ChIP-seq and ATAC-seq map epigenetic modifications throughout the genome by identifying DNA-protein interaction sites and open chromatin respectively, and although they capture different aspects of the epigenome, their resulting data share the same form and function (i.e. BAM files to capture reads, wiggle files to capture coverage and signal, BED files to capture peaks). Consequently, visualizing both types of data will follow the same workflow. We will start with the annotation from [Parsing GENCODE](@ref). Accompanying ChIP-seq data will be downloaded from the diff --git a/src/plotloops.jl b/src/plotloops.jl index cc0a044..bcd4069 100644 --- a/src/plotloops.jl +++ b/src/plotloops.jl @@ -4,6 +4,7 @@ function ellipse(x, a, b) end abs(b) * sqrt(1 - x^2/a^2) end + function drawloop!( ax::Axis, pairedends,