plot_profile: Logarithm of _P_-value (LOP) profile plots. Modified version...

In viewpoly: A Shiny App to Visualize Genetic Maps and QTL Analysis in Polyploid Species

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
)

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.

Value

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

viewpoly documentation built on May 29, 2024, 1:26 a.m.