Plot a genome scan

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"))