ggplot_pxg: Plot phenotype vs genotype

In qtl2ggplot: Data Visualization for QTL Experiments

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)

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