visualisePairing: Visualise pairing of parental homologues

In polyqtlR: QTL Analysis in Autopolyploid Bi-Parental F1 Populations

Visualise pairing of parental homologues

Description

Function to visualise the pairing of parental homologues across the population using graph, with nodes to denote parental homologues and edges to denote deviations from expected proportions under a polysomic model of inheritance

Usage

visualisePairing(
  meiosis_report.ls,
  pos.col = "red",
  neg.col = "blue",
  parent,
  max.lwd = 20,
  datawidemax,
  add.label = TRUE,
  return.data = FALSE,
  ...
)

Arguments

meiosis_report.ls	List output of function meiosis_report
pos.col	Colour corresponding to excess of pairing associations predicted (positive deviations), by default red
neg.col	Colour corresponding to lack of pairing associations predicted (negative deviations), by default blue
parent	The parent, either "P1" (mother) or "P2 (father)
max.lwd	Maximum line width, by default 20
datawidemax	This argument is currently a work-around to allow multiple plots to have the same scale (line thicknesses consistent). No default is provided. To estimate this value, simply set argument return.data = TRUE, and record the maximum absolute value over columns 'count', which are the deviations from random expectations. This should be done over multiple function calls if e.g. comparing both P1 and P2 values. When a global maximum (absolute) deviation is known, re-run the function with this value for datawidemax. The line width specified by max.lwd will then be used for this, and all other line widths re-scaled accordingly.
add.label	Should a label be applied, giving the maximum deviation in the plot? By default TRUE
return.data	Should plot data be returned? By default FALSE
...	Optional arguments passed to plot.igraph

Value

If return.data = TRUE, the values for pairwise deviations from the expected numbers are returned, useful for determining the value datawidemax to provide consistent scaling across multiple plots

Examples

data("mr.ls")
visualisePairing(meiosis_report.ls = mr.ls,
                 parent = "P1",
                 datawidemax = 3)

polyqtlR documentation built on May 29, 2024, 7:16 a.m.