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. 2015 Feb;199(2):359-61.
doi: 10.1534/genetics.114.172742. Epub 2014 Dec 18.

R/qtlcharts: interactive graphics for quantitative trait locus mapping

Karl W Broman  1
Affiliations

R/qtlcharts: interactive graphics for quantitative trait locus mapping

Karl W Broman. Genetics. 2015 Feb.

Abstract

Every data visualization can be improved with some level of interactivity. Interactive graphics hold particular promise for the exploration of high-dimensional data. R/qtlcharts is an R package to create interactive graphics for experiments to map quantitative trait loci (QTL) (genetic loci that influence quantitative traits). R/qtlcharts serves as a companion to the R/qtl package, providing interactive versions of R/qtl's static graphs, as well as additional interactive graphs for the exploration of high-dimensional genotype and phenotype data.

Keywords: D3; QTL; data visualization; software.

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Figures

Figure 1
Figure 1
A static view of an interactive graph for QTL analysis with a phenotype measured over time, with data from Moore et al. (2013) concerning root gravitropism in Arabidopsis recombinant inbred lines (RIL), Ler × Cvi. (A) Heat map of signed LOD scores for single-QTL analysis at each individual time point. Red indicates that RIL with the Cvi allele have a larger average phenotype; blue indicates that RIL with the Ler allele have a larger average phenotype. A is linked to B and C: when hovering over the heat map, the LOD curves for the corresponding time point are shown below in B, and the estimated QTL effect, as a function of time, is shown to the right in C. For the interactive version of this figure, see http://kbroman.org/qtlcharts/example.
Figure 2
Figure 2
Examples of the basic panels that form the core of R/qtlcharts. (A) Heat map; (B) LOD curves; (C) scatterplot; (D) a set of confidence intervals.
See this image and copyright information in PMC

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