plot_profile: Logarithm of P-value (LOP) profile plots. Modified version of QTLpoly function.

Description

Plots profiled logarithm of score-based P-values (LOP) from individual or combined traits.

Usage

plot_profile(
  profile,
  qtl_info,
  selected_mks,
  pheno.col = NULL,
  lgs.id = NULL,
  by_range = TRUE,
  range.min = NULL,
  range.max = NULL,
  plot = TRUE,
  software = NULL
)

Value

ggplot graphic (if plot == TRUE) or data.frame (if plot == FALSE) with information from QTL significance profile

Arguments

profile: data.frame with: pheno - phenotype ID; LOP - significance value for the QTL. It can be LOP, LOD or DIC depending of the software used
qtl_info: data.frame with: LG - linkage group ID; Pos - position in linkage map (cM); Pheno - phenotype ID; Pos_lower - lower position of confidence interval; Pos_upper - upper position of the confidence interval; Pval - QTL p-value; h2 - herdability
selected_mks: data.frame with: LG - linkage group ID; mk - marker ID; pos - position in linkage map (cM)
pheno.col: integer identifying phenotype
lgs.id: integer identifying linkage group
by_range: logical TRUE/FALSE. If TRUE range.min and range.max will set a colored window in the plot and the other positions will be gray. If FALSE, range.min and range.max is ignored
range.min: position in centimorgan defining the start of the colored window
range.max: position in centimorgan defining the end of the colored window
plot: logical TRUE/FALSE. If FALSE the function return a data.frame with information for only_plot_profile function. If TRUE, it returns a ggplot graphic.
software: character defining which software was used for QTL analysis. Currently support for: QTLpoly, diaQTL and polyqtlR.