Plot phenotype vs genotype

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.

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)))
#> Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
#> ℹ Please use `linewidth` instead.
#> ℹ The deprecated feature was likely used in the qtl2ggplot package.
#>   Please report the issue at
#>   <https://github.com/byandell-sysgen/qtl2ggplot/issues>.


# 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)

Usage

Arguments

Value

See also

Examples