ggplot_pxg {qtl2ggplot}

Plot phenotype vs genotype

Description

Plot phenotype vs genotype for a single putative QTL and a single phenotype.

Usage

ggplot_pxg(
  geno,
  pheno,
  sort = TRUE,
  SEmult = NULL,
  pooledSD = TRUE,
  jitter = 0.2,
  bgcolor = "gray90",
  seg_width = 0.4,
  seg_lwd = 2,
  seg_col = "black",
  hlines = NULL,
  hlines_col = "white",
  hlines_lty = 1,
  hlines_lwd = 1,
  vlines_col = "gray80",
  vlines_lty = 1,
  vlines_lwd = 3,
  force_labels = TRUE,
  alternate_labels = FALSE,
  omit_points = FALSE,
  ...
)

mean_pxg(geno, pheno, dataframe = NULL)

Arguments

geno

Vector of genotypes, as produced by maxmarg with specific chr and pos.

pheno

Vector of phenotypes.

sort

If TRUE, sort genotypes from largest to smallest.

SEmult

If specified, interval estimates of the within-group averages will be displayed, as mean +/- SE * SEmult.

pooledSD

If TRUE and SEmult is specified, calculated a pooled within-group SD. Otherwise, get separate estimates of the within-group SD for each group.

jitter

Amount to jitter the points horizontally, if a vector of length > 0, it is taken to be the actual jitter amounts (with values between -0.5 and 0.5).

bgcolor

Background color for the plot.

seg_width

Width of segments at the estimated within-group averages

seg_lwd

Line width used to plot estimated within-group averages

seg_col

Line color used to plot estimated within-group averages

hlines

Locations of horizontal grid lines.

hlines_col

Color of horizontal grid lines

hlines_lty

Line type of horizontal grid lines

hlines_lwd

Line width of horizontal grid lines

vlines_col

Color of vertical grid lines

vlines_lty

Line type of vertical grid lines

vlines_lwd

Line width of vertical grid lines

force_labels

If TRUE, force all genotype labels to be shown.

alternate_labels

If TRUE, place genotype labels in two rows

omit_points

If TRUE, omit the points, just plotting the averages (and, potentially, the +/- SE intervals).

...

Additional graphics parameters, passed to plot.

dataframe

Supplied data frame, or constructed from geno and pheno if NULL.

Value

object of class ggplot.

See Also

plot_coef

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)

# inferred genotype at a 28.6 cM on chr 16
geno <- maxmarg(probs, map, chr=16, pos=28.6, return_char=TRUE)

# plot phenotype vs genotype
ggplot_pxg(geno, log10(iron$pheno[,1]), ylab=expression(log[10](Liver)))

# include +/- 2 SE intervals
ggplot_pxg(geno, log10(iron$pheno[,1]), ylab=expression(log[10](Liver)),
         SEmult=2)

# plot just the means
ggplot_pxg(geno, log10(iron$pheno[,1]), ylab=expression(log[10](Liver)),
         omit_points=TRUE)

# plot just the means +/- 2 SEs
ggplot_pxg(geno, log10(iron$pheno[,1]), ylab=expression(log[10](Liver)),
         omit_points=TRUE, SEmult=2)