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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.

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Install

install.packages('qtlcharts')

Monthly Downloads

467

Version

0.16

License

GPL-3 | file LICENSE

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Maintainer

Last Published

January 7th, 2022

Functions in qtlcharts (0.16)

iplot

Interactive scatterplot
iheatmap

Interactive heat map
iplotCorr

Image of correlation matrix with linked scatterplot
ipleiotropy

Tool to explore pleiotropy
estQTLeffects

Calculate QTL effects at each position across the genome
cbindQTLeffects

Combine multiple runs of estQTLeffects
idotplot

Interactive phenotype x genotype plot
iboxplot

Modern boxplot linked to underlying histrograms
iplotMScanone

Interactive LOD curve
iplotCurves

Plot of a bunch of curves, linked to points in scatterplots
iplotMap

Interactive genetic map plot
setScreenSize

Set default maximum screen size
iplotRF

Interactive plot of recombination fractions
iplotScanone

Interactive LOD curve
qtlchartsversion

print the installed version of R/qtlcharts
iplotPXG

Interactive phenotype x genotype plot
scat2scat

Scatterplot driving another scatterplot
geneExpr

Anonymized gene expression data
grav

Arabidopsis QTL data on gravitropism
qtlcharts-package

R/qtlcharts: Interactive charts for QTL data
iboxplot_output

Shiny bindings for R/qtlcharts widgets
itriplot

Interactive plot of trinomial probabilities
iplotScantwo

Interactive plot of 2d genome scan