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R/qtlcharts: Interactive graphics for QTL experiments

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

install.packages("qtlcharts")

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

install.packages("remotes")

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

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.

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:

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.

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.

• D3.js (license)
• jQuery (license)
• jQuery UI (license)
• d3panels (license)

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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