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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.
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.
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)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.
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.