R/qtlcharts: Interactive graphics for QTL experiments
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.