R/qtlcharts: An R package for interactive QTL graphics
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Latest commit 89cc10d Jun 28, 2016 @kbroman Move vignettes out of package; just on website
 - Pains with CRAN; due to need to use configure script to rename a
   jQueryUI file with a really long name, I need to pre-build the
   vignettes (because when package is built, configure script is run and
   then vignettes are built, and then tar.gz file created, so that
   spoils my configure script thing)

 - So just moving all of the vignettes out of the package and onto the

 - Also added links to the vignettes in the qtlcharts-package Rd file


R/qtlcharts: Interactive graphics for QTL experiments

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Karl W Broman

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

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

For example charts, see the R/qtlcharts website.


Install R/qtlcharts from CRAN using


Alternatively, install it from its GitHub repository. You first need to install the R/qtl, htmlwidgets, and devtools packages.

install.packages(c("qtl", "htmlwidgets", "devtools"))

Then install R/qtlcharts using the install_github function in the devtools package.


Example use

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

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:

iplotCorr(geneExpr$expr, geneExpr$genotype)

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

# 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


The R/qtlcharts package as a whole is distributed under [GPL-3 (GNU General Public License version 3)[http://www.gnu.org/licenses/gpl-3.0.en.html].

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