Interactive Graphics for QTL Experiments

Web-based interactive charts (using D3.js) for the analysis of experimental crosses to identify genetic loci (quantitative trait loci, QTL) contributing to variation in quantitative traits. Broman (2015) .

Build Status CRAN_Status_Badge

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)[].

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


qtlcharts 0.11-6 (2019-02-04)

  • Fix bug in idotplot() so that it works with a single group.

  • Fix bug in iplotMap() so that the drop-down menu works in Firefox.

qtlcharts 0.11-4 (2018-03-08)

  • Update to use CoffeeScript v 2.2.2. Using babel to compile to ES5.

  • Switch from bower to yarn for javascript dependency management.

  • Revise scat2scat() so that the chart options xlab2 and ylab2 can be vectors of length of scat2data, so that each dataset can have different x- and y-axis labels. Default is to take them from the column names of the datasets in scat2data.

qtlcharts 0.10-1 (2017-06-01)

  • All charts can now take a heading and a footer within chartOpts. The former will make an <h2> heading above the figure; the latter will make a <div> at the bottom. These are intended for stand-alone html files.

  • In the caption chart option, now using .html() rather than .text() so that you can insert a bit of html (such as <b> or <code>).

qtlcharts 0.9-6 (2017-05-24)

  • All charts now can take a caption within chartOpts which will show up as text below the figure. This is intended for stand-alone html files.

qtlcharts 0.9-5 (2017-05-19)

  • Added new tool for exploring pleiotropy between two traits, ipleiotropy().

  • Fixed X chromosome case in iplotScantwo, so that only relevant two-locus genotypes are shown.

  • Added new chart option pointsize for iplotCorr.

  • In the coffeescript functions, ensure that list arguments like margin have all of the necessary components. This avoid the problem of everything being messed up if for example margin is specified within defining margin.inner.

  • lodcharts now includes a quantitative scale for position on the x-axis in the case of a single chromosome

  • In iplotScanone and iplotScantwo, in phenotype x genotype plots when switching between markers on the same chromosome, animate the movement of the points rather than destroying and re-creating the panel.

qtlcharts 0.8-2 (2017-05-11)

  • Updated to use D3 version 4.

  • Also updated d3panels, d3-tip, jquery, and jquery-ui.

qtlcharts 0.7-8 (2016-06-28)

  • Rewrite underlying javascript to use new version of d3panels.

  • Add a new chart, scat2scat. The idea is to summarize each of a long series of scatterplots with a pair of numbers. Then a scatterplot of those summary statistics is linked to the underlying details: click on a point in the main scatterplot and have the underlying scatterplot be shown.

  • Add a new chart, itriplot, for plotting trinomial probabilities, represented as points in an equilateral triangle.

  • Refactor iplotPXG and idotplot so that idotplot is the main function, and iplotPXG calls it.

  • Add some additional options, such as horizontal for iplotMap and iplotPXG.

  • Change the name of some options, such as linecolor and linewidth in iplotCurves (in place of strokecolor and strokewidth).

  • Add a digits argument for all plot functions, with the aim to reduce the size of the datasets included in the resulting charts.

  • Removed the vignettes from the package (for complicated reasons); they're available at the R/qtlcharts website.

qtlcharts 0.6-6 (2016-04-21)

  • Fix proliferation of tool tips

  • For use with Shiny, clear SVG before drawing

qtlcharts 0.5-25 (2015-11-09)

  • Skip Rmd and html tests run on CRAN (so faster, and because the Rmd tests won't work on Solaris as they need pandoc).

qtlcharts 0.5-23 (2015-11-07)

  • Changed license and author list in order to post the package on CRAN,

  • idotplot and iplot now use the names of the input data as individual IDs if indID is missing or NULL.

qtlcharts 0.5-18 (2015-09-02)

  • Fixed a bug in iplotScanone with pxgtype="ci". In the case of phenotypes with missing values, the confidence intervals were incorrect.

qtlcharts 0.5-15 (2015-06-24)

  • iplotCorr has argument scatterplots that controls whether scatterplots will be shown when clicking on pixels in the heatmap. (If scatterplots=FALSE, we skip the scatterplots.)

qtlcharts 0.5-13 (2015-06-08)

  • iplotMScanone can plot just points (rather than curves) for the LOD scores and QTL effects in the lower and right-hand panels.

  • Fix a bug in iplotMScanone (x-axis labels in right-hand plot weren't being shown)

qtlcharts 0.5-10 (2015-05-28)

  • Included bower information, about the javascript libraries, within the source package.

qtlcharts 0.5-8 (2015-05-13)

qtlcharts 0.5-4 (2015-03-10)

  • Added setScreenSize function for controlling the default sizes of charts.

qtlcharts 0.5-3 (2015-03-05)

  • Added idotplot function for plotting a quantitative variable in different categories. (It's just like iplotPXG, but with data values not connected to a cross object.)

  • Reorganized the d3panels code: just using d3panels.min.js and d3panels.min.css rather than linking to js code for individual panels.

qtlcharts 0.5-1 (2015-03-05)

  • Refactored the entire package to use htmlwidgets. A big advantage is that the charts now work nicely within RStudio.

  • To save a plot to a file, you now need to assign the result of a plot function to an object and then use the htmlwidgets function saveWidget.

    hyper <- calc.genoprob(hyper, step=1)
    out <- scanone(hyper)
    chart <- iplotScanone(out, hyper)
    htmlwidgets::saveWidget(chart, file="hyper_scanone.html")
  • It's now simpler to include interactive charts within an R Markdown document. You simply make the plots in a code chunk in the way that you would at the R prompt. There's no longer a need to worry about print_qtlcharts_resources() or results="asis".

  • Separated out the basic panel functions as a separate repository, d3panels, to make it easier for them to be used separately from R/qtlcharts.

Reference manual

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0.16 by Karl W Broman, 18 days ago,

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Browse source code at

Authors: Karl W Broman [aut, cre] , Michael Bostock [ctb, cph] (d3.js library in htmlwidgets/lib , , jQuery Foundation [cph] (jQuery library in htmlwidgets/lib , , jQuery contributors [ctb] (jQuery library in htmlwidgets/lib; see , jQuery UI contributors [ctb] (jQuery UI library in htmlwidgets/lib; see

Documentation:   PDF Manual  

GPL-3 | file LICENSE license

Imports qtl, htmlwidgets, graphics, stats, utils

Suggests htmltools, jsonlite, knitr, devtools, roxygen2, rmarkdown, testthat

See at CRAN