qtlcharts (version 0.16)

iplotRF: Interactive plot of recombination fractions

Description

Creates an interactive graph of estimated recombination fractions and LOD scores for all pairs of markers.

Usage

iplotRF(cross, chr = NULL, chartOpts = NULL, digits = 5)

Value

An object of class `htmlwidget` that will intelligently print itself into HTML in a variety of contexts including the R console, within R Markdown documents, and within Shiny output bindings.

Arguments

cross

Object of class `"cross"`, see [qtl::read.cross()].

chr

Optional vector indicating chromosomes to include. This should be a vector of character strings referring to chromosomes by name; numeric values are converted to strings. Refer to chromosomes with a preceding `-` to have all chromosomes but those considered. A logical (TRUE/FALSE) vector may also be used.

chartOpts

A list of options for configuring the chart. Each element must be named using the corresponding option.

digits

Round data to this number of significant digits before passing to the chart function. (Use NULL to not round.)

Details

The usual `height` and `width` options in `chartOpts` are ignored in this plot. Instead, you may provide `pixelPerCell` (number of pixels per cell in the heat map), `chrGap` (gap in pixels between chromosomes in the heat map), `cellHeight` (height in pixels of each cell in the cross-tabulation), `cellWidth` (width in pixels of each cell in the cross-tabulation), and `hbot` (height in pixels of the lower panels showing cross-sections of the heat map)

See Also

[qtl::est.rf()], [qtl::plotRF()]

Examples

library(qtl)
data(fake.f2)
fake.f2 <- fake.f2[c(1,5,13),]
fake.f2 <- est.rf(fake.f2)
# \donttest{
iplotRF(fake.f2)# }