ggplot_coef: Plot QTL effects along chromosome

Description

Plot estimated QTL effects along a chromosomes.

Usage

ggplot_coef(
  object,
  map,
  columns = NULL,
  col = NULL,
  scan1_output = NULL,
  gap = 25,
  ylim = NULL,
  bgcolor = "gray90",
  altbgcolor = "gray85",
  ylab = "QTL effects",
  xlim = NULL,
  ...
)
ggplot_coefCC(object, map, colors = qtl2::CCcolors, ...)
# S3 method for scan1coef
autoplot(object, ...)

Value

object of class ggplot.

Arguments

object: Estimated QTL effects ("coefficients") as obtained from scan1coef.
map: A list of vectors of marker positions, as produced by insert_pseudomarkers.
columns: Vector of columns to plot
col: Vector of colors, same length as columns. If NULL, some default choices are made.
scan1_output: If provided, we make a two-panel plot with coefficients on top and LOD scores below. Should have just one LOD score column; if multiple, only the first is used.
gap: Gap between chromosomes.
ylim: y-axis limits. If NULL, we use the range of the plotted coefficients.
bgcolor: Background color for the plot.
altbgcolor: Background color for alternate chromosomes.
ylab: y-axis label
xlim: x-axis limits. If NULL, we use the range of the plotted coefficients.
...: Additional graphics parameters.
colors: Colors to use for plotting.

Details

ggplot_coefCC() is the same as ggplot_coef(), but forcing columns=1:8 and using the Collaborative Cross colors, CCcolors.

Examples

Run this code

# read data
iron <- qtl2::read_cross2(system.file("extdata", "iron.zip", package="qtl2"))

# insert pseudomarkers into map
map <- qtl2::insert_pseudomarkers(iron$gmap, step=1)

# calculate genotype probabilities
probs <- qtl2::calc_genoprob(iron, map, error_prob=0.002)

# grab phenotypes and covariates; ensure that covariates have names attribute
pheno <- iron$pheno[,1]
covar <- match(iron$covar$sex, c("f", "m")) # make numeric
names(covar) <- rownames(iron$covar)

# calculate coefficients for chromosome 7
coef <- qtl2::scan1coef(probs[,7], pheno, addcovar=covar)

# plot QTL effects
ggplot2::autoplot(coef, map[7], columns=1:3)