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qtlcharts

R/qtlcharts: An R package for interactive QTL graphics

https://github.com/kbroman/qtlcharts

Science Score: 33.0%

This score indicates how likely this project is to be science-related based on various indicators:

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    codemeta.json file
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    .zenodo.json file
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    Found 3 DOI reference(s) in README
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    Links to: zenodo.org
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    1 of 3 committers (33.3%) from academic institutions
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    Low similarity (11.4%) to scientific vocabulary
Last synced: 10 months ago · JSON representation

Repository

R/qtlcharts: An R package for interactive QTL graphics

Basic Info
Statistics
  • Stars: 85
  • Watchers: 8
  • Forks: 29
  • Open Issues: 26
  • Releases: 0
Created about 13 years ago · Last pushed about 3 years ago
Metadata Files
Readme License

README.md

R/qtlcharts: Interactive graphics for QTL experiments

R-CMD-check CRAN_Status_Badge zenodo DOI

Karl W Broman

R/qtlcharts is an R package to create interactive charts for QTL data, for use with R/qtl.

It is built with D3, using a set of reusable panels (also available separately, as d3panels).

For example charts, see the R/qtlcharts website.

Installation

Install R/qtlcharts from CRAN using

r install.packages("qtlcharts")

Alternatively, install it from its GitHub repository. First install the remotes package.

r install.packages("remotes")

Then install R/qtlcharts using the install_github function in remotes.

r library(remotes) install_github("kbroman/qtlcharts")

The packages R/qtl and htmlwidgets will also be installed.

Example use

Try the following example, which creates an interactive chart with LOD curves linked to estimated QTL effects.

r library(qtl) library(qtlcharts) data(hyper) hyper <- calc.genoprob(hyper, step=1) out <- scanone(hyper) iplotScanone(out, hyper)

Also try iplotCorr, an image of a correlation matrix (for the gene expression of a set of 100 genes) linked to the underlying scatterplots, with the points in the scatterplot colored by their genotype at a QTL:

r library(qtlcharts) data(geneExpr) iplotCorr(geneExpr$expr, geneExpr$genotype)

Finally, try iboxplot, a plot of the quantiles of many distributions, linked to the underlying histograms.

```r library(qtlcharts)

simulate some data

n.ind <- 500 n.gene <- 10000 expr <- matrix(rnorm(n.ind * n.gene, (1:n.ind)/n.ind*3), ncol=n.gene) dimnames(expr) <- list(paste0("ind", 1:n.ind), paste0("gene", 1:n.gene))

generate the plot

iboxplot(expr) ```

Licenses

The R/qtlcharts package as a whole is distributed under GPL-3 (GNU General Public License version 3).

R/qtlcharts incorporates the following other open source software components, which have their own license agreements.

Owner

  • Name: Karl Broman
  • Login: kbroman
  • Kind: user
  • Location: Madison, Wisconsin, USA
  • Company: University of Wisconsin-Madison

Professor in Dept of Biostatistics & Medical Informatics at UW–Madison. Applied statistician working on statistical genomics.

GitHub Events

Total
  • Create event: 2
  • Release event: 1
  • Issues event: 1
  • Watch event: 2
  • Issue comment event: 1
  • Push event: 5
  • Fork event: 1
Last Year
  • Create event: 2
  • Release event: 1
  • Issues event: 1
  • Watch event: 2
  • Issue comment event: 1
  • Push event: 5
  • Fork event: 1

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 1,260
  • Total Committers: 3
  • Avg Commits per committer: 420.0
  • Development Distribution Score (DDS): 0.005
Past Year
  • Commits: 8
  • Committers: 1
  • Avg Commits per committer: 8.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Karl Broman k****n@g****m 1,254
Karl Broman k****n@b****u 5
timelyportfolio k****l@t****m 1
Committer Domains (Top 20 + Academic)
timelyportfolio.com: 1 biostat.wisc.edu: 1

Issues and Pull Requests

Last synced: almost 2 years ago

All Time
  • Total issues: 73
  • Total pull requests: 5
  • Average time to close issues: 4 months
  • Average time to close pull requests: 25 minutes
  • Total issue authors: 8
  • Total pull request authors: 2
  • Average comments per issue: 1.11
  • Average comments per pull request: 0.2
  • Merged pull requests: 4
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • kbroman (65)
  • raredd (2)
  • redsofa (2)
  • Shicheng-Guo (1)
  • SiddharthTomar (1)
  • aaronwolen (1)
  • simecek (1)
  • stephens999 (1)
Pull Request Authors
  • kbroman (4)
  • ghost (1)
Top Labels
Issue Labels
bug (37) enhancement (26) documentation (3)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • cran 690 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 1
  • Total versions: 10
  • Total maintainers: 1
cran.r-project.org: qtlcharts

Interactive Graphics for QTL Experiments

  • Versions: 10
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 690 Last month
Rankings
Forks count: 2.6%
Stargazers count: 4.4%
Average: 18.4%
Dependent repos count: 23.9%
Dependent packages count: 28.7%
Downloads: 32.3%
Maintainers (1)
broman@wisc.edu
Last synced: 11 months ago

Dependencies

.github/workflows/R-CMD-check.yaml actions
  • actions/checkout v3 composite
  • r-lib/actions/check-r-package v2 composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite
inst/htmlwidgets/lib/jquery-ui/bower.json bower
  • jquery >=1.6
DESCRIPTION cran
  • R >= 2.15 depends
  • graphics * imports
  • htmlwidgets * imports
  • qtl >= 1.30 imports
  • stats * imports
  • utils * imports
  • devtools * suggests
  • htmltools * suggests
  • jsonlite * suggests
  • knitr * suggests
  • rmarkdown * suggests
  • roxygen2 * suggests
  • testthat * suggests
inst/htmlwidgets/lib/d3/package.json npm
  • @rollup/plugin-json 6 development
  • @rollup/plugin-node-resolve 15 development
  • eslint 8 development
  • mocha 10 development
  • rollup 3 development
  • rollup-plugin-terser 7 development
  • d3-array 3
  • d3-axis 3
  • d3-brush 3
  • d3-chord 3
  • d3-color 3
  • d3-contour 4
  • d3-delaunay 6
  • d3-dispatch 3
  • d3-drag 3
  • d3-dsv 3
  • d3-ease 3
  • d3-fetch 3
  • d3-force 3
  • d3-format 3
  • d3-geo 3
  • d3-hierarchy 3
  • d3-interpolate 3
  • d3-path 3
  • d3-polygon 3
  • d3-quadtree 3
  • d3-random 3
  • d3-scale 4
  • d3-scale-chromatic 3
  • d3-selection 3
  • d3-shape 3
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  • d3-time-format 4
  • d3-timer 3
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inst/htmlwidgets/lib/d3panels/package.json npm
  • babel-preset-env ^1.6.1 development
  • d3 ^7.3.0
js_deps/package.json npm
  • @bower_components/jquery jquery/jquery-dist#^3.6.0
  • @bower_components/jquery-ui components/jqueryui#^1.12.1
  • d3 ^7.3.0
  • d3panels kbroman/d3panels#^1.8.4
js_deps/yarn.lock npm
  • @bower_components/jquery 3.6.4
  • @bower_components/jquery-ui 1.12.1
  • commander 7.2.0
  • d3 7.8.2
  • d3-array 3.2.2
  • d3-axis 3.0.0
  • d3-brush 3.0.0
  • d3-chord 3.0.1
  • d3-color 3.1.0
  • d3-contour 4.0.2
  • d3-delaunay 6.0.2
  • d3-dispatch 3.0.1
  • d3-drag 3.0.0
  • d3-dsv 3.0.1
  • d3-ease 3.0.1
  • d3-fetch 3.0.1
  • d3-force 3.0.0
  • d3-format 3.1.0
  • d3-geo 3.1.0
  • d3-hierarchy 3.1.2
  • d3-interpolate 3.0.1
  • d3-path 3.1.0
  • d3-polygon 3.0.1
  • d3-quadtree 3.0.1
  • d3-random 3.0.1
  • d3-scale 4.0.2
  • d3-scale-chromatic 3.0.0
  • d3-selection 3.0.0
  • d3-shape 3.2.0
  • d3-time 3.1.0
  • d3-time-format 4.1.0
  • d3-timer 3.0.1
  • d3-transition 3.0.1
  • d3-zoom 3.0.0
  • d3panels 1.8.4
  • delaunator 5.0.0
  • iconv-lite 0.6.3
  • internmap 2.0.3
  • robust-predicates 3.0.1
  • rw 1.3.3
  • safer-buffer 2.1.2