iplotScanone: Interactive LOD curve

In qtlcharts: Interactive Graphics for QTL Experiments

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
)

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 +/- 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.

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.

See Also

[iplotMScanone()], [iplotPXG()], [iplotMap()]

Examples

library(qtl)
data(hyper)
hyper <- calc.genoprob(hyper, step=1)
out <- scanone(hyper)

# iplotScanone with no effects
iplotScanone(out, chr=c(1, 4, 6, 7, 15))


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


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

qtlcharts documentation built on Jan. 8, 2022, 1:06 a.m.