ggplot_scan1: Plot a genome scan

In qtl2ggplot: Data Visualization for QTL Experiments

Plot a genome scan

Description

Plot LOD curves for a genome scan

Plot LOD curves for a genome scan

Usage

ggplot_scan1(
  object,
  map,
  lodcolumn = 1,
  chr = NULL,
  gap = 25,
  bgcolor = "gray90",
  altbgcolor = "gray85",
  ...
)

## S3 method for class 'scan1'
autoplot(object, ...)

ggplot_scan1_internal(
  map,
  lod,
  gap = 25,
  col = NULL,
  shape = NULL,
  pattern = NULL,
  facet = NULL,
  patterns = c("none", "all", "hilit"),
  chrName = "Chr",
  ...
)

Arguments

object	Output of scan1.
map	Map of pseudomarker locations.
lodcolumn	LOD score column to plot (a numeric index, or a character string for a column name). One or more value(s) allowed.
chr	Selected chromosomes to plot; a vector of character strings.
gap	Gap between chromosomes.
bgcolor	Background color for the plot.
altbgcolor	Background color for alternate chromosomes.
...	Additional graphics parameters.
lod	Matrix of lod (or other) values.
col	Colors for points or lines, with labels.
shape	Shapes for points.
pattern	Use to group values for plotting (default = NULL); typically provided by plot_snpasso internal routine.
facet	Plot facets if multiple phenotypes and group provided (default = NULL).
patterns	Connect SDP patterns: one of c("none","all","hilit").
chrName	Add prefix chromosome name (default "Chr").

Value

None.

See Also

ggplot_coef, ggplot_snpasso

Examples

# load qtl2 package for data and genoprob calculation
library(qtl2)

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

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

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

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

# perform genome scan
out <- scan1(probs, pheno, addcovar=covar, Xcovar=Xcovar)

# plot the results for selected chromosomes
chr <- c(2,7,8,9,15,16)
ggplot_scan1(out, map, lodcolumn=1:2, chr=chr, col=c("darkslateblue","violetred"),
     legend.position=c(0.1,0.9))

# plot just one chromosome
ggplot_scan1(out, map, chr=8, lodcolumn=1:2, col=c("darkblue","violetred"))

# can also use autoplot from ggplot2
# lodcolumn can also be a column name
library(ggplot2)
autoplot(out, map, chr=8, lodcolumn=c("liver","spleen"), col=c("darkblue","violetred"))

qtl2ggplot documentation built on March 31, 2023, 6:06 p.m.