r_LOD_plot: Plot r versus LOD

In polymapR: Linkage Analysis in Outcrossing Polyploids

Plot r versus LOD

Description

r_LOD_plot plots r versus LOD, colour separated for different phases.

Usage

r_LOD_plot(
  linkage_df,
  plot_main = "",
  chm = NA,
  r_max = 0.5,
  tidyplot = TRUE,
  nbins = 200
)

Arguments

linkage_df	A linkage data.frame as output of linkage.
plot_main	A character string specifying the main title
chm	Integer specifying chromosome
r_max	Maximum r value to plot
tidyplot	If TRUE (by default), an attempt is made to reduce the plot density using hexagonal binning from the ggplot2 package. This is recommended for large datasets, where the number of pairwise estimates becomes high.
nbins	The number of bins in each direction, passed to ggplot2::geom_hex. Only used if tidyplot = TRUE. Increasing this number can lead to slower but more accurate plotting.

Examples

data("SN_SN_P1")
r_LOD_plot(SN_SN_P1)

polymapR documentation built on June 22, 2024, 10:34 a.m.