iplotScanone: Interactive LOD curve

Description

Creates an interactive graph of a single-QTL genome scan, as calculated by [qtl::scanone()]. If `cross` is provided, the LOD curves are linked to a phenotype x genotype plot for a marker: Click on a marker on the LOD curve and see the corresponding phenotype x genotype plot.

Usage

iplotScanone(
  scanoneOutput,
  cross = NULL,
  lodcolumn = 1,
  pheno.col = 1,
  chr = NULL,
  pxgtype = c("ci", "raw"),
  fillgenoArgs = 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

scanoneOutput: Object of class `"scanone"`, as output from [qtl::scanone()].
cross: (Optional) Object of class `"cross"`, see [qtl::read.cross()].
lodcolumn: Numeric value indicating LOD score column to plot.
pheno.col: (Optional) Phenotype column in cross object.
chr: (Optional) Vector indicating the chromosomes for which LOD scores should be calculated. 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.
pxgtype: If phenotype x genotype plot is to be shown, should it be with means \(\pm\) 2 SE (`"ci"`), or raw phenotypes (`"raw"`)?
fillgenoArgs: List of named arguments to pass to [qtl::fill.geno()], if needed.
chartOpts: A list of options for configuring the chart (see the coffeescript code). 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

If `cross` is provided, [qtl::fill.geno()] is used to impute missing genotypes. In this case, arguments to [qtl::fill.geno()] are passed as a list, for example `fillgenoArgs=list(method="argmax", error.prob=0.002, map.function="c-f")`.

With `pxgtype="raw"`, individual IDs (viewable when hovering over a point in the phenotype-by-genotype plot) are taken from the input `cross` object, using the [qtl::getid()] function in R/qtl.

Examples

Run this code

library(qtl)
data(hyper)
hyper <- calc.genoprob(hyper, step=1)
out <- scanone(hyper)
# \donttest{
# iplotScanone with no effects
iplotScanone(out, chr=c(1, 4, 6, 7, 15))# }

# \donttest{
# iplotScanone with CIs
iplotScanone(out, hyper, chr=c(1, 4, 6, 7, 15))# }

# \donttest{
# iplotScanone with raw phe x gen
iplotScanone(out, hyper, chr=c(1, 4, 6, 7, 15),
             pxgtype='raw')# }