countmatrices.jl
Science Score: 41.0%
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Repository
Basic Info
- Host: GitHub
- Owner: CiaranOMara
- License: mit
- Language: Julia
- Default Branch: develop
- Size: 185 KB
Statistics
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
- Releases: 0
Metadata Files
README.md
CountMatrices.jl
The CountMatrices package handles the gathering and splicing of metadata into a count matrix.
Example workflow:
```julia using CountMatrices
using FileIO using GenomicFeatures # v3 using ColorSchemes
Define GenomicIntervals.
intervals = [ GenomicPosition("test1", 1, 1), GenomicPosition("test2", 2, 2), GenomicPosition("test3", 1, 3), GenomicPosition("test3", 3, 3), ]
Define various genomic windows.
windows = [ GenomicWindowCentred(GenomicPosition("test1", 2), Vector{eltype(intervals)}(), 1), GenomicWindowCentred{1}(GenomicPosition("test2", 2), Vector{eltype(intervals)}()), GenomicWindowCentred{1, Vector{eltype(intervals)}}(GenomicPosition("test3", 2)), ]
Collect intervals overlapping windows.
for (window, interval) in eachoverlap(windows, intervals) push!(window, interval) end
Sort windows to place the most significant at the top of the data matrix.
sort!(windows; by=window->sum(GenomicFeatures.volume, GenomicFeatures.metadata(window)), rev = true)
Splice windows into count matrix.
M = CountMatrix(windows)
Sort windows to place the most significant at the top of the data matrix.
M.m .= sortslices(M.m, by = sum, dims = 2, rev = true)
Get RGBA matrix.
path, io, c = draw(M; palette = ColorSchemes.balance, rangescale = :extrema, scale = log10)
Save colour matrix to file using FileIO.
save("heatmap.png", c) ```
Owner
- Name: Ciarán O'Mara
- Login: CiaranOMara
- Kind: user
- Website: https://ciaranomara.github.io
- Repositories: 102
- Profile: https://github.com/CiaranOMara
Citation (CITATION.bib)
@misc{CountMatrices.jl,
author = {Ciarán O'Mara <Ciaran.OMara@utas.edu.au> and contributors},
title = {CountMatrices.jl},
url = {https://github.com/CiaranOMara/CountMatrices.jl},
version = {v0.1.0},
year = {2023},
month = {4}
}
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| Name | Commits | |
|---|---|---|
| Ciarán O'Mara | C****a@u****u | 6 |
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